For which senses of simplified 制 would I use the traditional form 製? Simplified characters do not always mirror their traditional counterparts one to one. Sometimes you have a simplified character where some of its senses have one traditional form and some have another traditional form (essentially it's merged from multiple traditional characters). A very common example is 后, whose traditional form is 后 (same as the simplified form) for the sense of 'queen' and 後 for the sense of 'behind' or 'after'. 

My confusion arises with the simplified character 制. I can't seem to figure out for which senses the traditional form 製 applies and and for which ones it doesn't apply. For example, the word 制服, it seems to be written in traditional as it is in simplified sometimes: here (hk) and here (tw), whereas  other times, it's written as 製服 such as here and here (this page actually contains both instances!!). To further complicate things, 制服 has another unrelated verb sense meaning 'to overpower, to subdue' for which the traditional form is the same as the simplified form.

Can anyone shed some light on this for me?
Historically they were the same character. Later the meanings split, 製 is usually the verb meaning to make, and 制 the noun meaning the system, or more abstract things. 

Uniform should be 制服, because it means the clothing following certain rules/system. 製服 could be literally interpreted as clothing-making. Regarding the meaning of overpower, it must be 制服.