How to write out analysis of a game? I have read that one exercise to improve one's analysis/thinking skills is to set up a position, then write out and evaluate all the variations that could take place. Or write out analysis of one's own games (see for example this post). 

How do you actually write this out? Or better - how do good players usually write out their analysis?

I once tried it, but my paper soon became a jumbled mess. Particularly as you start to get branching lines and so forth it becomes hard to write and keep track of it all. Especially if you start writing out a line, but want to go back to a previous line. Is there some "special" method to write out analysis?
Computer Database programs (like the popular + free SCID) do the job pretty well provided you do not turn the engine on, nor have any other indicators (opening tree, endgame table bases etc.) enabled to distract you from focusing on writing down all the lines. 

I sometimes first do this in notepad as entering moves into a database allows you to see the pieces move, so it is cheating because you're not training your brain to visualize.  Once I'm confident of a line and its evaluation, I transfer it over to the database program.

Most DB software comes with nice bells and whistles for comments, variations, arrows/square highlighting as shown in the following example using SCID:



You can save each position into a file and collect oodles of these in a database for future review. Nice, clean and as organized as you can make it! 

What's nice is that once you are done, a strong player (preferred) can help critique this and you can add some more notes on where your analysis was inaccurate or just plain wrong.

As an added tip, make sure you start off with tactical positions (examples would be regular puzzles with a lot of forcing lines to calculate out) and then move towards rich analytical positions where there is no clear winning advantage in sight. NM Heisman's suggestion of the Stoyko exercises is definitely worth reading to get an idea of how to do this.

Update:

For non-software based ways of organizing analysis,  you can try mind-mapping but if that's too messy, why not derive inspiration from the popular MCO/NCO tabular-style of representing opening theory, for example: