text:
Should I simply ignore it if authors assume that I'm male in their response to my review of their article?
I received a response about a manuscript I reviewed earlier, and the authors write about the reviewer (i.e., me) and his concerns.  As a woman, I'm not so keen on this.
Obviously this isn't intentionally insulting or anything like that---it's a minor blip.  Nevertheless, it's a bit irksome, and the feminist in me is thinking that's not right; it's a microaggression (one of the everyday reminders that you don't belong here).
I could simply ignore it, but...
Question: Should I simply ignore it if authors assume that I'm male in their response to my review of their article?
There's no issues inside the manuscript: they thank the reviewers without using pronouns.
I'm particularly interested in if an editor would typically just groan and consider me a troublemaker for saying anything.  And probably not pass the message on to the authors anyway.

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As a reviewer, you are supposed to comment on academic value and scientific correctness of the manuscript.
As a woman, you feel unhappy about authors not guessing a correct pronoun for you and not using an appropriate gender-neutral pronoun.
It seems that the issue has nothing to do with the manuscript and hence you are not reacting with your reviewer hat on. You are considering your response based on your role as woman/feminist/activist — but not as a reviewer. You are not reviewing the paper, you are reviewing author's communicative behaviour.
As long as you make it clear that you are not commenting as as reviewer of a manuscript, I think you can make this remark to the editor.

On the one hand it's necessary to bring these issues up to improve the state of affairs.  On the other hand it probably won't benefit anyone if the reviewees is criticised directly because either a) they aren't being chauvanist, just thoughtless b) they aren't being chauvanist, just English-as-second-language c) they are_ chauvanist so will just discount the reviewer's comment.   I think that the best approach would be to address the response to the editor alone, and ask it as a question of some sort - "I notice that  said 'his' - do you think that that is just their idiom?"

Interesting answer - could you add an example text how one could formulate this ?

@Falco I could, however (1) I think it's best not to amend my answer to preserve consistency, and (2) it was OP's idea to write a message and OP is really the best person to write her messages as she knows all the specific details of her situation and I don't.

@Araucaria Would your feeling about the flavour as a woman in my text be the same if my name were feminine?

@Araucaria OP explicitly writes as a woman, I am not so keen on this. Obviously, OP is not content with the fact and considers to take an action, like writing to the editor. How is it a misattribution?

@Araucaria That's exactly what my answer says: As a woman, you feel unhappy about authors ... not using an appropriate gender-neutral pronoun, if you read the sentence in full. What is the misattribution?

@Araucaria It's only problematic because you selectively read a part of the sentence without full context. If you read the full sentence, it should not create any ambiguity beyond what is already contained in the OP's post. In any case, you claimed that as a woman was problematic first, and now your argument shifts, so I guess we have to stop here.

@Araucaria Since you keep changing your notion of what clause you find problematic, it is hard to see what you are suggesting. Maybe you can write your own answer?

I've found that some non-native English speakers use he for they, because that's how they'd do it in their mother tongue. Perhaps mention in your response (alongside any other language/style/etc.) issues:

Use they, rather than he, when the person's gender is unknown.

From chat:

Most native English speakers over a certain age were taught that the use of "they" to refer to a single person is incorrect (I continue to consider it incorrect).

Indeed, Strunk & White (The Elements of Style) write, "The use of he as a pronoun for nouns embracing both genders is a simple, practical convention rooted in the beginnings of the English language." They go on to add, "Currently, however, many writers find the use of the generic he or his to rename indefinite antecedents limiting or offensive."
But, "Singular they has become the pronoun of choice to replace he and she in cases where the gender of the antecedent – the word the pronoun refers to – is unknown, irrelevant, or nonbinary, or where gender needs to be concealed...that’s nothing new." The OED "traces singular they back to 1375, where it appears in the medieval romance William and the Werewolf."
See Wikipedia for a summary of guidance offered by style guides.

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I don't know what an editor would think of it, but I think it's fine to mention your experience of receiving the review with the incorrect pronoun, as long as (like other answers have said) you allow for the possibility that it was a translation error etc.
e.g.

...authors have addressed all issues...
PS. I appreciate this is a relatively minor issue, but as a female reviewer it felt awkward to be referred to as 'he' by the authors.

It may make more sense to do this if there is some action you would like the editor to take, e.g.

Would you consider issuing guidelines to authors and reviewers that they should not presume the gender of their colleagues?

I don't agree that as a reviewer/any other professional role you should have to ignore the discouraging effect that adds up from these interactions.

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I am not sure I would preface with either, "this is a relatively minor issue", nor with "as a female reviewer". Both cast the issue with your gender rather than the issue at hand which is one of presumption by the author. Nevertheless I agree that this is not something that should be ignored. And, in fact, should be highlighted.

Just drop it.
There are places where it's entirely reasonable for a scholar to start a discussion with a colleague about politically-charged, potentially-inflammatory topics such as microagressions, the appropriateness of using "he" as a genderless pronoun, unintended negative consequence of assuming a random member of a (presumably) male-dominated field is male, etc etc.
Reviewer-author communications are an especially poor choice of such a place.

Revealing information about your identity or ideological beliefs threatens your anonymity;
Peer reviews are intended to be objective, impartial, and impersonal, and political activism is decidedly off-topic in this context;
The review process is already often stressful and tense, and criticism of the author's communication style is more-likely-than-usual to be interpreted as confrontational rather educational.

EDIT: to answer your specific question: as an associate editor, I would do nothing: I would not delete a sufficiently civil correction in the “comments to authors,” nor would I relay anything to the authors if you put it in “private comments to the editor.” I would base all my decisions purely on the technical content of the review.

@user2357 even if the majority agree with your interpretation, a non negligible number of people will stridently insists that “I wasn’t assuming gender, I was using a gender neutral pronoun.” It’s just not the argument you want to start in the middle of peer review.

@user2357 You're assuming that they're assuming your gender, which is likely not accurate. While it's less common now than in the past, using the masculine personal pronouns as gender-neutral pronouns is still perfectly valid English and many people (especially from earlier generations) were taught this as being the correct set of pronouns to use. It is extremely likely that the author was neither intending offense nor assuming anyone's gender.

@user2357 I've almost consistently used he when referring to users in conversation on the internet, and I have never meant it to assume anyone's gender. If someone corrects me on their gender I accept it and carry on. And I don't treat it as a micro-agression or whatever. What I've come to notice is that people are more likely to use the pronoun that refers to them more often in such situations. There might be a psychological basis for that. I'm not certain. I definitely agree here though. Unless the replier knew their gender beforehand it's likely an unconscious writing habit.

Some comments deleted. Please keep discussion civil.

@user168715 A bit of a nitpick, but it's gender-indefinite, not gender-neutral. The former means you can use it when gender is unknown. The latter means you can use it even if gender is known.

The response doesn't have to be political or inflammatory. It's just a matter of tone.

If the use of the masculine pronoun to refer to a reviewer of unknown gender is problematic, this is so independently of the gender of the particular reviewer. A formulation like the following allows the reviewer to indicate this without revealing the reviewer's gender. In the reply to the authors the reviewer could write something like the following: Although the following comment is not relevant to my evaluation of the technical merit of the manuscript, the authors are advised that writing "his concerns" when referring to the concerns of an unknown reviewer presupposes that the reviewer is male, and that such an unfounded assumption could be bothersome to some reviewers.

While I may not agree with some of your comments above, I do believe this is a very reasonable answer to the question.

I'd suggest that the current italicized formulation (as of revision 1) makes assumptions about the authors' intent. The phrase "his concerns" might presuppose that the reviewer is male; it might alternately be used with gender-neutral intent because, until recently, prescriptive grammar taught people to use male pronouns for unknown individuals. With respect, stating these assumptions as fact might not adequately cover the possible scenarios. I can't seem to think of a formulation that covers both possibilities yet isn't cumbersome.

Minor point: the "and that" yields uncertainty: does it refer back to being advised, or to being presupposed?

I'd phrase it "could be bothersome to some reviewers.". Otherwise, it's also "gender assumption" thing but in opposite direction.

@Agent_L: I edited the proposal to make the change you suggest. Additionally, I don't pretend to offer a definitive wording, rather simply something viable, and what I've proposed surely can be improved in various ways.

If the editor forwards it, as an author, I would assume that the reviewer's gender is non-male after this comment, as the comment would be totally off-topic for the review otherwise. I don't think reviewers or editors would want to discuss such issues in the review, if there is no good reason to do so.

I do not think reviewers (and editors) would start to discuss something that's unrelated to the paper during a review, if there is no good reason for it. When a female reviewer feels addressed in the wrong way, it can be an issue, which is worth to be forwarded. If a male reviewer starts arguing "But I could be female and then it would be wrong …", this is a topic to be discussed at another place than during a review process. So assuming a serious review process, I would conclude from still getting this issue forwarded that there was a reason for it, which probably means a female reviewer.

I think you should let this one go.
If you have to use pronouns in situations where you don't know the author's gender, there's always a chance you get it wrong. For example take most questions here on Academia.SE. If you have to refer to the question-asker in a situation where the gender is unknown, do you use 'he' or 'she'? It's either choose one and risk the possibility of getting it wrong, or write 'he or she' everywhere and end up with a very cumbersome answer (not to mention there's still a chance you get it wrong, since it's possible the question-asker identifies as transgender and prefers 'they').
That said, you could write something like this:

The authors have addressed all the issues, and I recommend this paper for publication.
PS: I'm female.

Writing something short like this is unlikely to make the editor groan, and he or she (or they) will probably pass your comment on to the authors. Editors don't usually censor reviewers - that only happens if there's something really inappropriate in the review, and this certainly isn't something inappropriate.

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"P.S. I am a female" may lead to another issue: as women are underrepresented in many fields, and unfortunately math is one of them, in many areas a comment like this combined with the expertise needed to review the particular paper could likely identify the reviewer....

@NickS a field would have to be exceedingly male-dominated if there's only one woman who can review a paper though. If there're even two women, then it's still a 50% chance of wrong identification. I would be surprised, but it's up to Rebecca who'll know the field best.

I don't think mentioning that you are a woman would realistically enable someone to ''know'' who the reviewer is.

Should I simply ignore authors assuming I'm male in their response to my review of their article?

I wouldn't. But - I'd try to say something that sounds dispassionate and not very accusative. Paraphrasing @Allure's suggestion, and assuming the authors get a copy of your recommendation, I'd write something like:

The authors have addressed all the issues; the paper is therefore recommended for publication.
PS: In their response to the review, the authors assumed the reviewer was male (e.g. in using references such as "his concerns"). The authors are reminded that is not necessarily the case.

This has so far been mostly pointed out in the comments, but since comments get culled on topics like this, let me re-state it as an answer:

You don't know whether the authors are actually assuming your gender, or merely using a grammatical rule that you dislike, or aren't even fully conscious of their grammar (e.g., being non-native speakers).

Any response should take this into account: you don't want to assume what the authors are doing either. Thus, as several people on this thread have suggested (often for other reasons), it makes sense to be non-confrontative and not centralize the topic in your response.
The concept of a microaggression, too, does not have the empirical footing that it ought to have before I would start lobbing it as an accusation; google for "microaggression evidence" (e.g., Scott O. Lilienfeld, Microaggressions: Strong Claims, Inadequate Evidence). It isn't hard to draw some lines and define some things to be microaggressions, but the lines will depend heavily on who is drawing them, all while the actual damage done by crossing these lines is far from established. At the very least, the field isn't yet at the point where it can be applied with a resemblance of surety. Correspondingly, whatever you suggest should be a suggestion, not a correction.

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I think your question can be rephrased like this:
Should you do what you think it's right, or should you not, because it is likely to bite you back?
From my experience, nobody likes to be contradicted. Regardless of the context, or even the possible benefits that changing their minds can bring to them, people simply hate it to be contradicted. No matter whom (the journal, the authors, etc) you raise the issue, you'll be perceived as a pain in the ass, smaller or bigger, depending on how diplomatic you are.
What you need to do is to assess 2 things: what you lose and what you gain if you contradict someone. When assessing losses don't forget to include things like the spent effort (like posting this question here) and the virtual losses of debates which you may not have since the current loss will exclude you. When assessing gains don't forget to assess things like the societal impact.
In short: pick your battles. Only you can answer which are worth fighting for.
Edit: People keep misinterpreting my answer, which indicates that it is not clear enough. This is an attempt to clarify it.
Any answer that she should reply about the misuse of the pronoun or that she should let it go, is, in my opinion irresponsible. None of these 2 decisions can be reached simply by using the information provided in the answer. Such a decision should depend on many things, some of which are very personal details about the Original Poster (OP) (some examples are: is she currently involved in a lot of projects, is she currently over stressed, what is her relationship with the journal, does she care about it, can this affect her career, to what extent etc). Due to the nature of such details, I do not expect the OP to clarify the question, but to be helpful, I indicated a basic possible framework, which can help her reach a conclusion of her own.
Most people who already answered here believe she needs a push towards a decision, or a public poll on the matter. Her life is not a democracy, and her personal circumstances are not the same as other people circumstances. It is fair to say what one would do in her position, it is not fair to tell her what to do, from a selfish interest to promote the interests of the answering person, disregarding the possible detrimental effects on the OP and her agenda.
To exemplify, in her position, I would let it go, because I do not think that using the male pronoun as a neutral gender pronoun means anything more than that. I do not think it is non-inclusive, but a mere artifact of how English evolved over thousands of years. Even if it might have had non-inclusive origins (a fact that I do not know of) thousands of years ago, it does not have a non-inclusive meaning now. Still, I personally use they when the gender is not clear, because I know it might bother other people, and whether they are right or wrong, I still don't want to annoy them or disrupt the flow of whatever we were doing.
Even if in OP's position, I would let it go, I do not think that this is the best decision for her to take, because the optimal solution depends on her circumstances, of which I am not, and I cannot be aware of. Simply said, I am not her, and I encourage you, the OP, to carefully look inwards for an answer.
I hope that with my edit, which in my opinion, is just rephrasing and exemplifying my original answer, the answer is more clear now.

@StrongBad I did not consider it not nice, otherwise I would not have wrote it, but I'm not a moderator, so then it is not up to me to ultimately judge what's nice and what's not. You made a call, thanks for the edit. Edit: Apparently I can also edit other people's answers. I was not aware of this until now. Anyway, the edit stays.

Your edit definitely changes things (to me). It now gives an answer of what you would do and as such offered a course of action with an explanation of why. Your previous answer, was "In short: pick your battles ...". That is sound advice for many things in personal and professional life but doesn't really help most folks, imho. I've removed my down vote.

@Andrei yes with enough rep you can edit anyone's posts. I made the edit as a regular user and not with my super mod powers. The idea is for everyone to improve our community. Your further edits are great and I think this is now a really good answer.

"Most people who already answered here believe she needs a push towards a decision, or a public poll on the matter." <- Not sure why you're saying that.

+1, I don't agree with the idea that gender neutral "he" is inclusive, but strongly agree that people dislike being contradicted, and OP's dilemma is about balancing values with practicality. That OP even asked the question suggests that this value is pretty important to her, and probably out ways the practicality.

@CramerTV What I would do, is not relevant. That is why I didn't initially include it. I do not try to persuade the OP to do what I would do. Obviously, now that it's out there, it might influence the OP in a way which might be detrimental. I tried to avoid that. As you said, pick your battles is sound advice for many things in personal and professional life, why wouldn't something you say is sound advice be helpful?

Apply Hanlon's razor with great liberty. It is most probably thoughtlessness in this case.
Peer-review is supposed to be a neutral and objective process, which involves the authors not communicating directly with the reviewers. Thus, the authors most probably had no idea you are a woman.

I don’t think OP is assuming malice. It’s fairly reasonable to still want to correct this incorrect usage, regardless of intent.

However, reviewers are supposed to be anonymous to the authors of the paper. Thus, correcting the use of gender-related pronouns reveals the identity of the reviewer to a certain extent, especially in fields with little women in top positions. If at all, such a correction should be handled by the editor, which leaves open the possibility that the author referred to reviewer B as he, while in truth reviewer D is the woman.

A fair consideration that perhaps reduces the blame from the original author, especially if there was a language issue. Clearly the anonymity must be limited, if the OP is certain the comment in public record refers to her assistance. If there is anonymity during the review process, that suggests there is also moderation where the OP's name has later been inserted, and the moderators clearly need reminding that female invisibility is not acceptable.

Firstly, I would check whether the journal has a policy or style guidelines to the effect of using gender-neutral pronouns, and whether the authors are native/non-native speakers of English. If, as you say, you have met one of the authors, you probably can make a strong guess at their nativity.
Case 1: Non-native speaker
Many (I would hazard a guess and say most) non-native speakers, myself included, have been taught never to use "they" in singular. In fact, we received corporal punishments at times if we did that. I learnt about this usage only after I relocated, and since then I've had to consciously convince myself to use it. Secondly, some of the non-English languages I speak, don't have or usually use gender-neutral pronouns. Although that is changing, they are far behind on the curve than English is. Hence, in the case of non-native speakers, I would probably give them a large benefit of doubt.
In this case, I suggest that you write to the editor separately. If they don't have a policy, request that they make one. If they do, explain your experience without naming names and request them to enforce it better.
Case 2: Native speaker
This is would be a more egregious case since we can assume that the person at least knows of this usage, and there's not much room for doubt. In this case, I would go with something like what @user100093 suggests in his answer, except I would modify the 'P. S.' section to say - "This is a relatively minor issue, but I would appreciate it if the authors don't assume the gender of the reviewers in their responses or communications". That way you have made your point without revealing your own gender, thus preserving anonymity.
As to whether the editor would actually pass on the message to the authors - who knows. But I don't believe that you will be immediately branded a troublemaker simply for making this point.

Having any P.S. at all would hint that OP is a woman, since no man would add a P.S like that. ... There's basically no way to assert any of OP's characteristics without scratching away anonymity.

"This is would be a more egregious case since we can assume that the person at least knows of this usage, and there's not much room for doubt." As a native speaker, I'd disagree. While most native speakers are 'aware' of the gender-neutral 'they' and will understand it, many (especially from older generations) still dislike it, consider it grammatically incorrect, and don't use it. There is a reason your English courses taught you that this usage is incorrect. It's because many native English speakers do still consider it incorrect, even if I'd personally disagree with them.

@Malandy For what it's worth, I call out every single instance of gendering I see in responses to my reviews with a note similar to TheJack's suggestion — even though they always correctly assume that I am a man.  It is not appropriate for them to bring an imagined gender into things with my reviews, just as it is inappropriate with Rebecca J. Stones'.

I'd like to write more or less what Dmitry Savostyanov wrote in his answer

It seems that the issue has nothing to do with the manuscript and hence you are not reacting with your reviewer hat on. You are considering your response based on your role as woman/feminist/activist — but not as a reviewer. You are not reviewing the paper, you are reviewing author's communicative behaviour.

but without the last part where he suggests that

As long as you make it clear that you are not commenting as as reviewer of a manuscript, I think you can make this remark to the editor.

I believe the professional thing to do in this context is just ignoring the pronoun, without any remark whatsoever.
It's curious that this question comes more or less at the same time as this one: How to react to a student proselytising during office hours? . I think the two settings are more similar than it seems at first sight. This is a context in which you should focus on content and stick to business, not try to convince the paper's author of his/her mistakes on a matter unrelated to the content of the paper, even if you believe it's for the greater good.

It's interesting that you draw that parallel with the proselytization question, because there, everyone seems to agree that when the OP says "I don't want to be put in a similar situation again", there is some right not to be put in that situation, and so the OP should address it directly.  Yet here, the OP has been put in a situation she dislikes (and likely will be again in the future), and only speaking up has any chance of changing that, but is being advised that she should not speak up.  She's not the one creating this situation; the authors using a masculine pronoun are.

@Mike I am not comparing OP here to the professor in that question, I am comparing her to the student. The student tries to convince the professor of his/her mistakes in not following the cult of Cthulhu the Almighty; the fact that there are so many unbelievers is a situation he dislikes, and he believes he is acting for the greater good.

I understood what you were trying to imply.  What I am saying is that you choose to overlook the fact that the OP here did not ask to be referred to in the masculine; you're suggesting that she's starting something by responding to unprofessional behavior.  Apparently the other OP had not brought up any religious beliefs whatsoever before the student started proselytizing.  Similarly, this OP had not brought gender into the discussion before she was referred to with a male pronoun.  In both cases, the OP has been subjected to something they find unpleasant and unprofessional.

@Mike I think the consensus here is that the use of that pronoun is probably involuntary. It's OP who is planning to bring gender into the discussion and derailing what has been up to now a professional exchange.

Well, to bring up a point that only seems to have been in comments...
If you don't care about your anonymity, or those whose anonymity partially depends on your anonymity, then go ahead and say you're a woman.
Else, you might have to say nothing, because by making a note about gendered pronouns, could be taken to hint that you are a woman, because a man is assumed to be less likely to bring the topic up.
Although, men do make such notes, as Mike says in his comment:

I (a man) always tell authors who refer to me by gender that it is inappropriate to bring an imagined gender into a technical discussion.

Is this blind-bag reviewing, or not?

In a sufficiently small academic community, revealing one's identity compromises the anonymity of others. 2. Pointing out usage of a gendered pronoun reveals nothing about one's own gender

@trichoplax - How... Oh, okay, adding 1. ... On 2. ... It feels more likely that more women would find the gendered pronoun notable than men would, so pointing out the usage hints that the speaker is a woman?

I don't have statistics to say either way, but it may well be that in a field with more men than women, there are more men objecting to gendered pronouns than women. But even in a field where an objector is statistically more likely to be female, only a likelihood is being revealed, not a concrete gender. Also there are plenty of men who feel strongly about this, and plenty of women who don't care either way.

As I mentioned in another comment, I (a man) always tell authors who refer to me by gender that it is inappropriate to bring an imagined gender into a technical discussion.  This is just one more way in which it's a bad idea to try to divine the referee's identity by over-interpreting details in the response.  In any case, what better time to try to effect change than in an anonymous setting?

@Mike - Thank you! Added to the answer. Not sure how to use the rest of your comment since it seems off-topic from the core of my answer. You do raise some good points.

I encourage you to speak up.  As you suggested, it's probably fair to think of it as a minor slip-up, indicating ignorance or implicit bias rather than overt bias or intent to harm — so your response should probably treat it as such.  But nothing will improve if we stay silent.
Below I'll say how I might respond, but first I want to address the many wrong-headed arguments against responding that I've seen on this page, so I'll make a list and respond to each.  I'll be paraphrasing, but I think these are fair representations of the various points.

English evolved over centuries to arrive at gender-neutral "he".  English evolved in societies that were generally swamps of overt misogyny.  The fact that the patriarchy has always done it this way doesn't mean it should always be done this way.  Nor do modern notions of equality expunge history of its inequalities.  When Thomas Jefferson wrote that "all Men are created equal", women really did not have equal rights (not to mention non-white or even just non-rich men), and it's silly to pretend that we're doing anything but rewriting the text by interpreting that to include women.
There's no good alternative.  Many of the comments have refuted this pretty well.  Pronouns can be avoided altogether by talking about "the reviewer" or similar.  Alternatively, singular "they" is actually deemed acceptable by many authorities, and will get the point across in any case.
The authors might have a different first language where default-masculine is totally standard throughout many of their language structures.  That's fine, but now they're communicating in English — and in a professional setting.
But the authors weren't even assuming your gender.  That doesn't matter; it's still problematic to use "he".  While ethicists will talk about intent being important for deciding whether or not an action is ethical, there are also considerations about reckless disregard for the consequences.  Reckless homicide is still homicide.  If they offended you by their reckless and unnecessary use of a masculine pronoun (minor though the offense may be), it was still offensive.
Not everyone can agree that what they did was problematic.  That's true, just as not everyone can agree that it wasn't problematic.  We fight for our own principles.  If we only stood up on unanimous decisions, we would never stand up — and there would be no point anyway.
It's too minor to bother with.  As you said, it's really about your status as a full and equal member of your community — which is not minor.  You deserve respect.
Don't start trouble.  You're not the one who started it.
An academic review isn't the appropriate venue to introduce your feelings or politics.  Again, you didn't start this; the authors are the ones who acted unprofessionally by introducing some imagined gender.  They communicated poorly, and it is absolutely a reviewer's job to suggest improvements and to act as the arbiter of standards in the community.  Suppose they had said something that was clearly intentionally and extremely racist.  Would it still be inappropriate to address the matter?
You'll harm your professional relationships.  This is anonymous review.  The editor you're dealing with is the only person who will know who you are, and in my experience they are professionals who understand that they need to keep things professional — though it is true that highly specialized journals survive because they are run by individuals who are in that specialized field, and thus may be more likely to encounter you personally, in which case you may need to use your judgment.  The authors won't know who you are, and might just become more conscientious in their treatment of women in your field — possibly including you personally.  If you can't speak up now, when can you?
You'll pierce the veil of anonymity by revealing your gender.  You don't need to refer to your gender at all.  I'm a man, and I always advise authors who refer to me using a gender that it's not professional.  I don't recall ever mentioning my gender when I did that.  In any case, revealing your gender would only be a partial piercing of that veil, narrowing down the list of possible reviewers to people who might care about this sort of thing.
You can't change anything.  In each case where I've advised authors not to use masculine pronouns for anonymous reviewers and where there's been another round of revisions (so that I saw a response from them), they've apologized and said they won't do it again.  I can't say whether they took the lesson on equality to heart, but as long as their words change that was a positive outcome.
They don't deserve to be punished for your feelings.  This isn't punishment; this is a very private communication, limiting the extent of any embarrassment or any other consequences they may experience.  Whereas many commenters here are suggesting that their use of the masculine is not a big deal, I would also point out that your response will not be a big deal.  All you're doing is giving them a tiny bit of sound advice.  And this isn't just about feelings; it's about equality in the workplace.

So we're left with the conclusion that we really should say something, but the issue is what to actually say.  I can't claim to have the optimal solution, but I can say what I do in this situation and what my reasoning is.  I generally write something along these lines after anything else I have to say:

In their response, the authors referred to the anonymous reviewer's concerns as "his" concerns, despite not knowing the reviewer's gender.  The use of masculine pronouns in gender-neutral situations is no longer considered correct in modern English, and is generally perceived as unacceptable in a professional setting.  In cases like this, it would probably be more effective to write things like "the reviewer's concerns".  Though this is a minor issue, we all need to be careful and make an effort to maintain a professional and inclusive environment for the benefit of our shared field.

Though the wording is a bit awkward in places, I have some motivation for it.  Obviously, I want to get the point across without the authors becoming defensive.  So I start off by stating the facts as plainly as possible — they really did write that, and didn't know the reviewer's gender.  Then I de-personalize it by using the passive voice and referring neither to the authors nor to myself; I talk about things like "correctness" and "professionalism" to point towards external standards that are generally accepted rather than some random reviewer's idiosyncrasies.  I suggest a more appropriate alternative, couching it as "effective" in an effort to appeal to practical-minded authors.  I make sure to say that this is a minor issue because (as evidenced on this page) some people may overreact and take it as a personal accusation of some grave moral defect or an implication that the authors are irredeemable monster; it's just a one-off mistake made by people who are probably quite decent individuals.  I try to defuse potential defensiveness by including myself and saying "we" have to do this and by talking about the benefit of our shared field.  And I say that we need to be "careful" and "make an effort" to suggest that these things aren't always obvious and automatic.
Again, though, that's just what I would write.  Some commenters have suggested that you might specifically say that you are a woman.  I can't claim to have any insight on that; I can imagine it might be counterproductive for anyone not inclined to agree with you anyway, or it might be persuasive to people who didn't realize actual women might feel this way, or maybe it'll just plain make you feel better for standing up for yourself (which is also a valid objective).  You're the best judge of that.  In a similar vein, while I don't want to start tone policing, I'll just point out that this page also demonstrates that some people are triggered by words like "feminist", "misogynist", and "microagression" (not to mention "triggered"), which can push the discussion toward derailment.  Evidently, people get distracted by the words themselves.  They fail to notice that you use them not as some sort of rationale for why you should feel this way, but in an effort to communicate what you actually do feel; the communication breaks down.  While I find such objections childish and feeble-minded, there's no arguing with the fact that they occur.  And if you want to maximize your likelihood of making a positive impact, it may be better to avoid them.  So sticking to your specific feelings in this particular case, rather than appealing to the more general context, would be the more effective path.

I like the assembled arguments and counter arguments that you've put in this post. But, while there's a strong hint of what you propose (you list reasons that refute all the arguments against responding), you never explicitly include an advice on what to do. If you could collect your suggestion in one final paragraph and maybe propose how you would respond (e.g. "I would include, as a last comment to the authors, a remark that I find using gender pronouns in their response is unprofessional, without mentioning my gender", plus a potential phrasing to would use), this would be a great answer.

@penelope Thanks.  I've added the sort of thing I write in these cases, and a [possibly too-detailed :)] explanation of my reasoning.

some people are triggered by words like "feminist" and "microagression" -- speak for yourself. Lots of people see the words for fashionable markers that have lost their meaning (feminist) or ideological shibboleths whose validity rests upon assumptions swept under the carpet (microaggression). You could equally well argue I'm "triggered" by the word "synergy" because every time I hear it, I can't help wonder what BS I'm being sold (despite the real meaning that this word might have in a better world).

Thanks for the addition, I really like this answer now. Your wording in the proposed response might be a bit too verbose for my style, but the reasoning is great, and would allow anybody to write a similar (or shorter) response in their own style. And as always, the answers to "controversial" questions are more likely to attract both up- and down-votes I guess...

I realized a long time ago that there's very little to be done in situations like these, because regardless of what you say, they can always resort to the grammar-defense: he is an accepted pronoun in the case of gender-neutrality, so in their eyes, they're just speaking English.
It doesn't cross their mind that, hey, negro is an accepted English word as well, so maybe it would be acceptable to use that word to describe black people too, no? Of course, today, that wouldn't fly: we live in a world where that word is no longer acceptable.
Similarly, all you can do is wait until people evolve enough until the consensus changes in favor of they, and not he, as the appropiate gender-neutral pronoun. There's definitely a clear trend towards they, so it might happen sooner than you think, but, really, waiting is all you can do. Making a fuss about this is going to make people become defensive (because personal egos are more important than deep societal issues) and that isn't going to end well for you.

It's not even about singular "they", which some may find awkward. A simple "he or she" would also work. But you can't do that because... grammar.

@SAK I disagree with your conclusion.  You don't avoid using the word negro because people shut up and waited for change.  Why would the change have happened, except that people explained that they found it offensive?  If, in the authors' eyes, "they're just speaking English", then how could they possibly realize that anyone wants that particular usage to change unless they are told?

@Mike You've misunderstood the answer. Let me break it down for you: in this particular context (a one-off professional, indirect correspondence with anonymous authors through a 3rd party editor), there's little you can do, and even if you tried, you'd be shut down and refuted immediately. In other contexts, you may be able to do more, in which case, my advice of just waiting obviously ceases to apply. It is in this way that change occurs: because there are certain contexts where people do (and should) speak up. But that doesn't mean you should be doing it 24/7.

For example, writing this question which has been viewed 22.000 times has caused change, I guarantee you ... much more than would have been achieved if she had made a fuss in her particular situation.

I disagree that she can't change anything directly.  I (a man) always correct authors who refer to me using gender, and explain that it is not appropriate to assume gender of an anonymous reviewer.  This happens to me frequently, and I have received responses from authors who apologize and suggest that they will avoid it in the future.  It may well be true that the authors were pandering to me by apologizing, but what matters to me is that they likely really will avoid it in the future because a colleague has told them it is unacceptable.  And the fewer people who have to face this the better.

I assume there is an editor. So I would ask the editor to let the referee know that their readership and authors are male and female and they should not presuppose a male author through the use of their pronouns. This way you don't embarrass the referees and also don't enter into confrontation with them.

I'm going to suggest something a bit different - others have hinted at this, but really there are two activities here that are being terribly conflated and should really be addressed completely separately.
As far as this specific review goes, I would completely drop it.  The issue is not relevant to the review whatsoever and there are enough unknowns here to preclude your knowing the author acted out of malice (which, in fact, it is most likely the opposite case - that they wrote this with your identity being no more than an anonymous talking head and without giving it a second thought).  This is issue one.
The second issue is your desire to raise awareness about gender issues in academia generally.  This is doubly so the case if we default to the assumption that the original author was not being malicious but rather just defaulting to a perfectly normal standard of language which appears to be falling out of popular favour (and which you would like to change).
Consider now the second goal and the things you might do to effectively achieve that goal.  What will it achieve to write a letter to the author?  The editor?  Probably close to nothing, and you risk introducing confusion and uncertainty into the review process.  Going straight back to the author or editor here is a high-controversy, low-impact action.  You won't change many peoples' ideas and you risk exposing yourself to blowback.
If this is an issue that is important to you I would suggest that you take this up as a completely separate activity entirely disconnected from this specific review.  If it's an issue with one journal, surely it must be an issue with all journals and reviewers and authors in the field.  Do you want to spend time and effort changing one author's mind? Or one journal's?  Or do you want to actually do something effective to promote this type of change across the field?
I feel your efforts would be better rewarded by focusing them away from this specific review - why not completely independently make contact with all of the major journals in your field?  Raise it as an issue on its own and pursue it on its own merits - this turns it into a general issue rather than a specific one (which you might be seen to have a conflict of interest regarding the particular review in question).

I'm not really sure I personally agree to this answer (the OP cares and is considering taking action regarding this issue, or, rather, instance; suggesting that she either should do more or nothing at all is a bit... pushy), +1 because it's a well argumented and presented different perspective.

@penelope I understand that OP cares about this specific incident.  I guess my point is that, regardless of that, there are few actions that can be taken which with any probability to produce a positive outcome.  Raising awareness behind closed doors isn't something that ever happens.  You take on all the risks of taking a stand and don't really have anything substantial to profit from it.

The person is not necessarily assuming you are male. Similar to what you encountered, many women use "she" or "her" when the gender is unknown. Not using a pronoun in that spot may have made the sentence structure read awkwardly, and they might not be aware of the increasing use of "they" in such a case.
I have had women use "she" or "her" when writing about me when they did not know that I was male. I was annoyed for just a few seconds, until I realized that I occasionally do the same thing in reverse, and for that reason I have started using "they" as a gender-neutral singular pronoun. But not everyone does that.
In short: They might not be assuming you are male, but they had to write something in that spot.

I've also seen many male authors use it when writing articles because female empowerment, or something along those lines.  Or worse still—alternating between the two on every occasion a pronoun is used...

How often was the possessive adjective "his" or pronoun "he" used? Once, twice or several times? It sounds like it was used once.
The OP acknowledged it was probably a simple mistake, a minor blip so she should treat it like one. Ignore it.
If it happens again with the same author(s), she should not shy from pointing out "their" repeated and unintentional blunder to the editor or in a friendly personal email.

This is an issue that is best addressed through the editor of the journal. Ultimately  the best solution might be for a revision of the "Guide for Authors" noting the correct form of address (i.e., "reviewer one," "reviewer two," or "they"). A revision to the "Guide for Authors" would also allow editors more opportunity in the future to correct authors to ensure appropriate forms of address.
While the desire to address the author is understandable, I don't see how it could be done without violating any of the types of blind review:

Single Blind - They might now know enough to tell who you are in a field with low representation.
Double Blind - Same as single blind, plus for reasons that other answers have noted, you shouldn't be assuming their national origin.
Triple Blind - Same as above, plus the editor now has enough information to maybe guess who you are.

Another consideration is if the author sees your feedback along with a reject notice from the editor. Depending upon their basis, they might assume that you were unduly harsh in your review because of the microaggression. It's also going to be a one-way communication which generally makes for a poor learning experience on the part of the author.

Depending on culture the response may be male dominated and therefore the term 'he' is used mindlessly, and especially if the gender is unknown. Names don't give away gender all the time either - especially across cultures.
The term reviewer would be neutral.
There are some points of issue: Are you on a face-to-face known basis or simply on a web distance unknown basis?
If you are not on a face-to-face basis with someone then it may not be important and depending on how your gravy train works it is probably not important.
However if you are known face to face - then sure you might mention you do like to be referred to as she and not he.
In some terms let us put it this way if you are receiving work because of a 'perception' don't kill your gravy train. You KNOW who you are (or maybe not and that is the issue).
Perhaps you want to be recognized as a woman achieving, and not simply as a person achieving?
If someone is presenting an award - one likes to be referred to correctly, but if they pay me 2 million dollars and refer to me as she did an excellent job.. well I certainly did and thank you.
They may get the gender wrong but the pay and the accolade was correct. Better than $0 and saying Sally did such a wonderful job ... just missed the mark completely.
Again if I am on the web writing some code for someone and they are paying me and saying she is fantastic - well, maybe it is a typo, maybe not .. but hey I don't know them personally and maybe they feel comfortable working with a she. I am not going to tell them nor will I tell them if I am Jewish, Chinese, or whatever. I want the work and they can say man that Indian guy is doing great work...As long as they pay me and keep sending me requests for jobs...

This is a reasonable general answer about the workplace but misses the academic nuances and the specifics about the relationship between a reviewer and an editor and authors.

@StrongBad you are correct, B/C the op does not state 'the specifics about the relationship between a reviewer and an editor and authors' .
In other words how these people are known or spread across distance or organization(s), neither the specifics of the environment. So I had hoped some general guidance may be of use to the op in determining a course of action.
Her editors may (depending on relationships etc) simply ignore her comments (out of convenience ie the importance test). At which point the short answer is ignore it, let it ride,blow it off.

@StrongBad I'm curious what "nuances" and "specifics" you refer to here. As it stands, and as far as I can tell, the question is a classical example of a boat programming question, in that it is totally unrelated to academics in particular and could equally refer to an "accountant and a manager" or a "retail seller and shop owner", and thus, is blatantly off-topic. Maybe you can enlighten me in how far the question is related to any of the topics mentioned in the help center.

@Marco13 reviews are supposed to be impartial and related to the work and avoid personal issues. The reviewer is supposed to stay anonymous and conversations with the editors are generally very limited/non-existent. The number of potential reviewers is limited and there is potential for backlash. If this was a colleague using the wrong gender in a meeting, it would be more general to the workplace. Finally, there is a lot of microagression and sexism in the academic workplace, so even if the question was of general interest, it seems a very good fit here.

@StrongBad The anonymity/backlash issue looks like a valid point. But at this level of analysis, it has to be considered in similar forms in similar situations, and as such, is not specific to academia. The broader question is whether someone should complain about everything that she considers as a "microaggression". You can find this everywhere if you're actively looking for it and want to stir things up (that's what I wanted to point out by mentioning the "editress"...). Whether this sort of question and the attention does not do more harm than good? Time will tell. I'm worried.

@StrongBad your quote: 'reviews are supposed to be impartial ... The reviewer is supposed to stay anonymous and conversations with the editors ...'  The answer is then quite clear Keep Silent. Further a cultural & gender neutral pen name would be better.

This answer is barely coherent and doesn't suggest the answer-er even knows what peer review is.

@AzorAhai Where does the op state Peer Review? In peer review the data and conclusions are examined. In reviewing a manuscript the grammatical correctness, readability is what is being evaluated; these are two different things. Read the ops question again - you will find the terms editor, author , reviewer and manuscript - all suggestive of editorial review. In either case speak up and kill the gravy train for no reason . Further the editor may not pass anything along to anybody or the authors may simply ignore/forget or pay no attention to the request. In either case speaking up did nothing.

@Ken Who do you think does "editorial review"? This is a site for people to get expert answers, not guesses from people unfamiliar with academia.

@Ken The question leaves no room for doubt that the OP indeed did refer to "peer review". Clarity of presentation was always part of peer review - data and conclusions need to be both clear and correct. The fact that journals are increasingly expecting the authors and reviewers to take care of grammar and typesetting is a long-know creeping problem. Mentioning the "gravy train" implies you think the OP is being paid for this review - which is almost never true for peer review. It seems, from your answer and comments, that you are not familiar with the academic publishing and review process.

If the answer to the reviewer was restricted in length (based on characters), my suggestion is to ignore it.
In that case, "he" is simply one of the shortest pronouns available in English, and in length-limited texts, every character may count when struggling for including another statement relevant to the content of the paper or of the review.
That doesn't mean there are no better choices available, such as using "R" to refer to the reviewer (or "R1", "R2", ..., in the case of multiple reviewers) in a stylistically clumsy (based on current preferences, where repeated mentions of the same object are typically substituted with pronouns - this may be changing, of course), but short and gender-agnostic way.

Could any of the downvoters explain what is wrong with this answer, please?

I'm still considering whether to downvote this or not (I haven't yet and find it borderline), my two issues with your answer are: a) you're only offering an answer for one specific and not very common case (a very small to negligible portion of the reviews I did were length limited and usually allowed attaching a pdf or text file with the response), so it's a very partial answer, and b) I personally don't agree that using they over he is a problem even in character limited reviews - the pronoun is not going to be used more than a handful of times, producing an overhead of ~10 characters.

@penelope: I understand. For a), I think this is very field-dependent. In my CS subdiscipline, length limitations are pretty much the norm. Reviews and author responses are typically entered in web-based forms, and if you exceed the length limit, you simply cannot submit your input. Likewise, coming from a field with strict length limitations (in characters and/or pages), the ~10 characters you mention in b) seem like a valuable resource to me that can mean adding or dropping one or two significant words. I fully agree this answer applies only to certain fields; given the differences ...

... between academic disciplines and cultures, I think it is often the case here on Academia SE that for a single question, very different answers are actually the "best" answers depending on the specific preconditions from certain fields or countries.

Once again, I'd ask the downvoters to explain what is wrong with this answer. I am rather baffled about the negative response this is receiving. Is there any factual problem with what I have written?

I haven't cast any vote but I disagree with the assertion and justification "he" is simply one of the shortest pronouns available in English So is "it" and while we are at it "she" just adds a single character, I hardly think typing "she" requires that much more effort, time or space. I dislike  the solution of acronyms "R1" "R2" etc.  it feels impersonal and dehumanizing (just throwing out some ideas as to why the downvotes).


text:
How to get covered in non-academic media
Scientists and other academics often embark on studies or make research findings of interest to a wider audience of laypeople.  Sometimes this work gets covered in media devoted to pop science or pop culture (Popular Science, Quirks and Quarks, etc.), and sometimes even in general-purpose news magazines and newspapers like TIME and The New York Times.
If your peer-reviewed research has produced something likely to be of interest to the general public, what are the best ways of bringing this to the attention of non-academic media outlets?  I imagine networking could play a big role here (that is, once you've been covered in the media once, you could contact the same journalist with news about related research by yourself or your colleagues).  But what if you have no prior contacts?  Do newspaper editorial desks welcome tips for science/humanities research stories the same way they do for general news events?  Is it a faux pas to write an enquiry directly to a magazine journalist who has previously covered research in a related area?  If a press release is the way to go, exactly how and where should it be posted or submitted?

I suspect the PR or Marketing department of your university would be very keen to help you place a story and advise you on writing for the media.
In every University I have worked in, this has been important, and media training was part of the staff development program. I was sent on a BBC media training course, for example, and can now operate a remote radio or TV studio, learn how to be an interviewee or interviewer and record students and staff for media inserts.
Tabloid writing was a skill I also picked up which is so different from academic writing. Learning to write in a style that the bulk media might pick up and use is not a natural skill for the everyday academic.
So go and ask. Might be fun.

Press releases are important for getting widespread attention.  If your university is anything like U.S. universities, then they will have a PR office that can help issue press releases.  Of course they won't do it unless they feel there's a plausible story, but if they do then they can be extremely helpful.  Some top journals (such as Science and Nature) also try to pitch stories to the press, with embargoed access to papers before publication.
It's absolutely critical to think about timing.  At least in the U.S., science journalists care a lot about newsworthiness.  If they are writing about a single paper, then they generally want the story to come out when the paper is published, rather than a month later.  (In some cases, they would lose interest even a week later.  The only way they will maintain sustained interest over time is if the story is extremely important.)  If they are writing about a larger trend, then they want their story to appear while the trend is still new and surprising, rather than being a retrospective account.  This is radically different from how scientists typically think about public communication.  We'd like to see stories that teach the public something valuable, regardless of how fresh and newsworthy the topic is, but journalists lose interest incredibly quickly.

Is it a faux pas to write an enquiry directly to a magazine journalist who has previously covered research in a related area?

It usually is.  My understanding is that science writers get a lot of unsolicited requests to write articles on the requester's work, and having to deal with this does not make them happy.  Instead, you can build contacts in other, more constructive ways.  One is to offer tips for hot stories on other people's work.  Of course you should do this exceedingly sparingly, but if there's a major breakthrough in your field that is very recent and exciting and has not yet had any news stories on it, then that could be a useful tip.  Another way to get your name out there is by being interviewed.  Your university PR office may be able to connect you with journalists as an expert they could interview regarding stories in your field.  It wouldn't be about your work, but it would get you some attention, and if you impress the journalists they are more likely to remember you and pay attention to your work in the future.
Having a high-profile science blog is also a good way to attract attention from journalists, since it establishes you as an expert who can communicate well with the public (which is ideal for getting good quotes).

If a press release is the way to go, exactly how and where should it be posted or submitted?

You shouldn't do this yourself, since it would look tacky.  If your university or publisher is willing to do it, then they will know how, so you should ask them.  (But don't bother asking the publisher unless it's a fancy journal that is used to doing this.)

Is it a faux pas to write an enquiry directly to a magazine journalist
  who has previously covered research in a related area?

No, there is no harm in writing an editor with a story idea, but keep in mind that editors are looking for stories and writing styles that appeal to their audience.
Keep in mind the 7 news values:

Impact: the number of people influenced by the subject of the story
Timeliness: recent events have a higher news value
Prominence: people in the public eye have higher news value
Proximity: stories about events and situations near home are more newsworthy
Bizarreness: man-bites-dog is more interesting than dog-bites-man
Conflict: public anger or disagreement over fundamental issues
Currency: stories about issues currently in the public spotlight

So with that in mind, the likelihood that your recent conference paper on a theory for a new space elevator -- though revolutionary -- will be front page news of the Wall Street Journal is next to zero... but if you founded a company to build a space elevator and you're prepping for an IPO, than that might get some prominent placement. Then again, the conference paper about space elevators might get some coverage in Popular Mechanics.

If a press release is the way to go, exactly how and where should it
  be posted or submitted?

Those are pretty much guaranteed to go into the trash. Nobody reads those things in a newsroom. There are just too many cheap, online PR companies offering to spin those things out full of fake quotes and exaggerations. I have seen them used more frequently in the business world by prospective applicants looking to make their name more prominent in a Google search, or posting that stuff on their LinkedIn and personal website to make themselves look good... but it looks cheap and artificial.
My advice would be to start a blog featuring your work and covering the work of others in the field. Think and act like a journalist: talk to people, interview people, write stories, explain the big picture and provide lots and lots of visuals.
There are fantastic examples of this sort of working coming from the cartography and data science communities. Those guys are bootstrapping to try and create a name for themselves, and its working very well. A few years ago, you'd have to be familiar with scripting and programming languages to make those visuals work, but there are lots of free services to get around that.
Your blog entries don't have to be masterpieces of fine art. Keep it short, timely, and within the public interest.

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text:
Value of listing OEIS contributions on an academic CV
The Online Encyclopedia of Integer Sequences (OEIS) is a large online database of number sequences.  It's popular among professional and amateur mathematicians, and its entries are widely cited.  Like Wikipedia, most of its content is authored and edited by the community; no particular qualifications are required to participate, though in my experience most active editors are working mathematicians or scientists.
I've occasionally seen academic CVs which list OEIS contributions among the publications (usually in a separate subsection).  I've also seen CVs of known contributors which make no mention whatsoever of their OEIS contributions.
I was wondering, then, whether listing OEIS contributions is generally a good idea when applying for academic jobs such as post-docs and professorships.  How much weight, if any, do recruiting committees in math and computer science place on OEIS contributions?  Are they viewed as minor professional publications, as non-academic community service, or as unwanted and annoying CV padding?
Related question: Value of contributions to Wikipedia when applying for academic jobs

Important: separate section.  So no one thinks you are trying to sneak them in as equal to publications.
Probably it will have no weight for recruiting.  I suppose having the list there may cause someone on the committee to say "I've heard of this guy."
But CVs have uses other than job searches.  So go ahead and include them if you want to.

This kind of contribution is important and not as much credited as it should be. But I wouldn't suggest to include single contributions to OEIS or other things like that in a CV. Two reasons:

You are not the author and it's an impossible task to include the author list.
It clutters the CV and makes it unreadable long.

However, it deserves its space. In Economics, there is often a section in CVs called Service. It is about refereeing activities and faculty jobs. I would mention there that I contribute to OEIS or Wikipedia. Alternatively, you mention it on your personal website. Recruites look there, too.

Why do you say that those who write OEIS entries are not authors?  What else would they be?

Well, I don't know exactly how OEIS works, but when it's like Wikipedia, I'd say: it's hard to say when a contributor is an author. And to be honest (in a CV), the author would have to name all other authors as well.

I have already published 16 sequences on it and only in one case I was named as coauthor because one of the editors joined with me for completing the work and in all the rest I am the  author. If you define the sequence and could able to find the terms, that honour should be given to you. Am I wrong?

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text:
Should I normalize inconsistent proceedings titles?
I work in a discipline where titles of published conference proceedings are notoriously inconsistent.  (Perhaps all disciplines are like this?)  For example, various years' proceedings of the same annual event may be officially titled a dozen different ways:

Proceedings of the First Annual Conference of the Society for Underwater Basket Weaving
Proceedings of the 2nd Conference of the Society for Underwater Basket Weaving
Proceedings of the 1998 Conference of the Society for Underwater Basket-Weaving
SUBW '99: Proceedings of the Annual Conference
Papers from the Fifth International Conference for Underwater Basket Weaving (SUBW 2000)
Society for Underwater Basket Weaving: Papers from the 6th Annual Conference in Ashgabat, Turkmenistan
SUBW 2002: Past Successes and Future Directions
(etc. etc.)

Sometimes the titles aren't even consistent in the same volume of proceedings—different names may appear on the cover and the inner title page!
My question is, where one's publisher expresses no preference on how one's bibliography is formatted, is it better to keep such titles as-is, or to normalize them?  For example, one possible way of normalizing the above entries would be as follows:

Proceedings of the 1st Annual Conference of the Society for Underwater Basket Weaving (SUBW 1996)
Proceedings of the 2nd Annual Conference of the Society for Underwater Basket Weaving (SUBW 1997)
Proceedings of the 3rd Annual Conference of the Society for Underwater Basket Weaving (SUBW 1998)
Proceedings of the 4th Annual Conference of the Society for Underwater Basket Weaving (SUBW 1999)
Proceedings of the 5th Annual Conference of the Society for Underwater Basket Weaving (SUBW 2000)
Proceedings of the 6th Annual Conference of the Society for Underwater Basket Weaving (SUBW 2001)
Proceedings of the 7th Annual Conference of the Society for Underwater Basket Weaving (SUBW 2002)

The disadvantage of doing this is that your bibliography is no longer an accurate reflection of what's printed in the proceedings themselves.  If any libraries hold copies of the proceedings, they may catalogue them under the original titles, so a reader wouldn't be able to find them there by searching for one of your normalized titles.
However, I think normalization has some significant advantages.  For one, it's always clear which conference of which scholarly society you are referencing—something which isn't always the case when using the original titles.  Since many proceedings nowadays are published online only, normalizing the titles could make it easier for readers to find the society's web page, and through it the proceedings.  Nowadays many proceedings can be uniquely identified by ISBN or DOI; including these identifiers in the bibliography makes it less important to faithfully transcribe the title.  Using consistent titles also makes it easier for readers to search your bibliography for references to papers in proceedings volumes of interest, without having to know or remember their original titles.
A third option would be to list both the original title and the normalized version, though I think this is rather cumbersome, particularly when the two versions differ only slightly.
Am I missing any more advantages or disadvantages?  Do any popular style guides speak to this issue?

I would think “annual conference” is not going to appear in the title of the first one and then disappear in subsequent iterations. Usually it’s the other way around. :p

The Conference on Precision Electromagnetic Measurements (CPEM) is one conference in my field that suffers from the same problem, complicated by the fact that the proceedings are called conference digest, instead (digest is put sometimes at the beginning, sometimes at the end). I have never seen works from this conference cited in the same way, and given that this conference started in 1962, if there were serious problems in finding the proceedings in the libraries, probably some form of standardization would have come out along the years.
In general, I try to be consistent, at least within a paper. Your example, composed of both the full and the abbreviated titles, seems fine to me: in any case it gives the reader, even one not familiar with your field, all the possible search keys to identify the volume (and one familiar with the conference would probably not care anyway).

One issue is setting precedents for reporting inaccurate bibliographic information.  Some authors are sloppy or eccentric, and I don't want to offer them any flexibility or encouragement.  (Of course some of them will be sloppy or eccentric anyway, but it's still useful to have a clear rule.)  Even for careful and sensible authors, it can be difficult to judge what the most recognizable, searchable, or useful form of a title is.  The answer may be rather different for experts and non-experts, or now vs. a hundred years in the future.  Standardizing on the exact title as published is the simplest and most systematic way to resolve this issue.  To the extent there's a consensus on this issue, I believe it's using the original title.  (A bibliographic entry should be a factual assertion.)
You can always add clarifying information in square brackets as you see fit.  For example, you could append "[SUBW 2001]" to "Society for Underwater Basket Weaving: Papers from the 6th Annual Conference in Ashgabat, Turkmenistan".
The trickiest case is when a conference's name has actually changed.  For example, the Symposium on Switching Circuit Theory and Logical Design, Symposium on Switching and Automata Theory (SWAT), and Symposium on Foundations of Computer Science (FOCS) are all the same conference at different points in time.  It would be really problematic to standardize "Third Annual Symposium on Switching Circuit Theory and Logical Design 1962" to "3rd Annual Symposium on Foundations of Computer Science (FOCS 1962)".  That would be in line with the present-day conference name, but it would be incredibly confusing for anyone who actually looked the paper up and found no mention of FOCS at all.
Of course the examples listed in the question are substantially less problematic, but I feel it's safest to draw the line at the actual title.

Sorry, but this seems like it will create, rather than prevent, chaos. If you don't use the "official" name of a conference or its proceedings and, instead, use one that you prefer, you create two negative effects.
First, you complicate search. People reading your work will want to check your references. Without the official titles, this becomes harder. Giving both the official and your "preferred" title just makes things messy, not neat.
Second, if you can do this so can others. So, you "regularize" a list of conferences in one way and I "regularize" it in a different way. Again, chaos.
But perhaps the names are given for a purpose that you don't recognize or understand but you want to place your judgement over those of a lot of other people, including the conference committees and the organization's officers.
If you want the stated problem to go away, then work within the sponsoring organizations to regularize the names of things so that the issue starts to go away.

I agree with this answer, and just want to note that one additional thing one may consider doing is put an explicit note in the bibliography that the conference proceedings have gone by a variety of names and you are explicitly using the official name of each.

Without the official titles, this becomes harder — [citation needed] First, Google is actually quite good at finding the right title, even if you get it slightly wrong.  Second, even publishers themselves are inconsistent; for example, ACM conferences often have slightly different titles on the actual physical cover, in the ACM Digital Library, and in DBLP and other standard indexes.


text:
Differences between German computer science doctorates
The faculties of some German universities offer a choice of doctoral degrees.  For example, Technische Universität Darmstadt's Department of Computer Science allows candidates to apply for either a Doktor-Ingenieur (Dr.-Ing.) or a Doctor rerum naturalium (Dr. rer. nat.).  Candidates choose which degree they want to apply for shortly before they submit and defend their thesis; the only guidance provided is as follows:

Der Dr.-Ing. wird im allgemeinen auf Grund einer Dissertation
  verliehen, die überwiegend ingenieurwissenschaftliche Erkenntnisse aus
  der Informatik enthält.
Der Dr. rer. nat. wird im allgemeinen auf Grund einer Dissertation
  verliehen, die überwiegend theoretische wissenschaftliche Erkenntnisse
  aus der Informatik enthält.

Roughly translated:

The Dr.-Ing. degree is generally awarded on the basis of a thesis that contains predominantly engineering-related findings in computer science.
The Dr. rer. nat. degree is generally awarded on the basis of a thesis that contains predominantly theoretical scientific findings in computer science.

Other German universities may offer yet other degrees.  I know some computer scientists who hold a Dr. phil. (Doktor der Philosophie).
In some cases where the university offers various doctoral degrees, a thesis may meet the criteria for several of them.  (For example, in the TU Darmstadt example, the thesis may contain engineering-related and theorical scientific findings in roughly equal proportions.) In such cases, is there any reason for the candidate to prefer requesting one degree over the other?  Do the various computer science degrees have different standings or reputations?  Will having one or another make it easier or harder to get certain types of jobs in academia or industry, either in Germany or abroad?

In general, the latin title of the degree conferred at a German university is of purely historical relevance (basically, indicating how the original four faculties of the middle ages split into the dozen or more departments of today, which happened in different ways at different universities -- obviously, Computer Science split off of Electrical Engineering in Darmstadt, rather than, say, Mathematics as in Munich); the important information is which department conferred the degree (which differentiates a Dr.rer.nat in Mathematics from one in Physics or Chemistry).
There is, however, one exception: The Dr.-Ing. (Doctorate in Engineering) still has a special place as an indication of the high regard in which German academic engineering is held (mostly, needless to say, within Germany, as well as by those directly influenced by this system, although a hundred years ago this was indeed something special), and is the reason why Darmstadt is offering a choice -- in effect, it's a marketing strategy to get students to enrol by offering them a degree that's perceived as more attractive. (This is also related to the fact that some universities still hand out "Dipl.-Ing." diplomas even though the Bologna process turned every other degree into a Masters.)
As to whether the choice of degree will make a practical difference in finding a job, that's hard to say. My feeling is that it will most likely play a role when transitioning to industry in Germany, where someone with a Dr.-Ing. might be seen as more "hands-on", practical-oriented, than with a Dr.rer.nat. (especially at small or medium-sized companies which might hesitate to hire a purely theoretical PhD). On the German academic job market, on the other hand, the university (and research group) where you got your title would be much more important. Outside Germany, I'd be surprised if many people cared much about the distinction (unless they themselves are the proud holders of a Dr.-Ing., of course...)

From my experience the flavour of your Dr. does not really matter when looking for a job in the (technical) industry. I am unsure if this also applies for academia.
In general a Dr.-degree is seen as a proof that you are capable of scientific work over a long period (including sustained motivation and organisation).
As it will most likely make you experience your own boundaries you should not chose the flavour of your degree by anything other than your personal interests and preference.
Your preference as well as the working environment should influence your choice more than letters after the hyphen.

While the exact type of Dr. degree typically have a small influence on your future there is one thing to be careful with. Check the official translation of the degree into English. Some universities have chosen to translate the engineering degrees to "Doctor of Technology", which can be a headache when moving to a country where this is not a recognized degree. It's typically easier if the degree is translated to Doctor of Philosophy by the university.


text:
How can I find good examples of transdisciplinary literature reviews?
I'm planning on writing up a narrative literature review for publication as a journal article.  The topic is a transdisciplinary one, and so I'd like the review to cater to academic audiences across these disciplines, which poses certain challenges for how to style and structure the review, what sort of content and context to include, etc.  I'd like to see some good examples of how others have handled such reviews so that I might learn from them and perhaps adopt/adapt some of their features.
Apart from searching citation indexes like Google Scholar for terms like "transdisciplinary literature review" and browsing the results for relevant, highly cited papers, are there any other ways of finding high-quality examples?  For example, are there any books or online resources about writing literature reviews that cite some highly regarded examples?  Are there any such reviews that have won best paper awards or the like?

I suggest you go talk to the university "research" librarian. This is what they do.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is "academic incest" a concern with research grant applications?
A colleague and I, early-career researchers, are planning to submit a research funding proposal.  The research program we are envisioning would need a third PI with complementary expertise and resources.  Of all the collaborators we might invite, one of the most qualified would be our former supervisor.  (I worked under this supervisor as a doctoral researcher, and my colleague and I both worked under this supervisor as postdocs.  All three of us are now at different institutions across Europe.  My colleague and I have each already received a single-PI research grant without any involvement of the former supervisor.)
The funding program to which we are applying indicates that its purposes are only "to support excellent collaborative research projects" and "to make it easier for researchers to collaborate across borders", so including our former supervisor doesn't violate any explicitly stated guideline.  However, I understand that "academic incest" is often a concern, for example when admitting graduate students or hiring faculty.  Is it also a concern when evaluating research funding proposals?  That is, is it possible/likely that reviewers would raise objections to a funding proposal that is submitted jointly by a professor and two of their former postdocs?  If so, we'd rather invite a different collaborator to be the third PI and retool the research program around their particular skills and resources.

There are issues beyond the funding mechanism you need to be concerned about here -- specifically, your tenure committee when you come up for review.  They will be looking for evidence that you've successfully established your independence as a scientist.  If this grant is your only major initiative, and it looks like you need the support of your mentor, you may have a problem.
That said, a portfolio can be a big complicated thing.  If there are other factors that clearly establish your strengths as a successful independent researcher, there may be no cause for worry.
The tenure clock ticks fast, and establishing collaborations beyond your mentor quickly is something worthy of your attention and efforts.

Since decisions are made by individuals with their own priorities (and biases) I can't say that it isn't a concern, but it should be a minor one, especially as you state the case.
A more important expectation of those judging whether to give money for a given project is whether these people are likely to do a good job with the proposed research (and the money). An established collaborative group probably sits a bit higher on that scale than an untested one. These folks have worked successfully together in the past and are therefore more likely to do so in the future. Equally important is whether this research is really worth doing at all (with our money).
I worry about your suggestion of choosing people first and then choosing the direction afterwards. That feels backwards. If you have a good research question, a plan to work it, and a good team, I see no reason to do otherwise.
And, regarding your examples of academic incest, some of them are actually based on similar considerations, not incest. A person is known to a supervisor or hiring committee already as a successful and compatible researcher. Yes, we will choose them over an unknown.
There are, of course, true instances of academic incest, with unqualified people selected for reasons other than merit. But I don't think it applies to your case.
OTOH, there is also merit in bringing new people into an existing collaboration. Those are often students, in fact.

Thought experiment: Imagine a world in which there was active discrimination of existing successful collaborative groups in favor of new and untested ones. Would scholarship likely be improved in such a system?


text:
Is there a trollish/novelty/esoteric citation style?
In programming, there are these so-called "esoteric  programming languages" like "LOLCODE" or "Shakespeare," which really have pretty much zero usefulness. They are just kind of a novelty, or if a computer science professor is feeling like being particularly obnoxious he can choose it as the language for one of his assignments.
I was wondering if there is anything similar for citation styles. Citation styles are a "language" of sorts, and in principle you could have the analog of "LOLCODE" for making citations. I have never heard of such a thing, and I was considering inventing one---you know, something for a Humanities professor to require if they are feeling like being particularly obnoxious---but I wanted to make sure that such a thing didn't already exist.

I'd say, any of the traditional styles that includes a requirement for listing the city a publisher is located in.  In our digital and globalized society, how is it even meaningful to talk about "the" location of a major international publishing house?

That at least used to have a legitimate reason (or so I've heard): that printings of the same book in different cities wouldn't necessarily be the same, so you had to know which city the book came from to make sense of a reference. Of course this hasn't been a valid reason for a very long time.

@jakebeal see this question on using city of publication in citation

If you want to troll, you can do this well enough with any given style. Just cite a 600-page textbook without giving any section or page numbers, or cite a published version with a page number coming from the arXiv preprint. Also "and references therein" :)

May I humbly suggest footnote labyrinths?

Alt text: Every time you read this mouseover, toggle between interpreting nested footnotes as footnotes on footnotes and interpreting them as exponents (minus one, modulo 6, plus 1).

Off the top of my head, an esoteric citation style would be one that uses exclusively doi and/or ISBN numbers instead of author-year or similar styles ---e.g., "as doi:16.1244/0979e.98 says in his reply to 12-9809-090-09..."

In a similar vein, academic books should have (author, year) inline citations. Numeric inline citations are bearable for a 10 page academic paper -- they are incredibly annoying for a 200 page book.

Don't forget to make them non-clickable and non-copypastable in your pdf file, for addded trolling value.

@AndyW: Your mileage may vary. I find it a lot more convenient to remember a three or four digit number for the short period of time that I need to open the appendix section than an arbitrary name and a year. The same goes for finding the respective reference in a bibliography spanning many pages at the end of a book.

The syntax of .bst files (bibtex style files) is obscure enough to be borderline to an esoteric programming language, in my opinion. Example here.
(And don't get me started on TeX error messages...)

Your own .bst for pretty documents? It's not for the faint of heart. It's just not.

Ah BAFLL...happy memories :)