So I had to dig through a quick and dirty project and document it from scratch. Checked out Doxygen and wow. Those are my experiences so far:
The good: Provides nice and easy documentation (even readable in the code!), is quite flexible and has tons of cool features, but most important: DOES WHAT IT'S SUPPOSED TO (:3 on this)
The bad: Some tags aren't that intuitive, at least not for me - and you do quite some workaroundish stuff, until you realize that there is a simple "\exactlywhatyouneed" - maybe I'm just slow
The ugly: Some things cannot be done through the huge, awesome config file. E.g.: I tried aligning a image I used on the left side. Not a chance - This stuff is hardcoded and you have to use a dirty css hack to get in running ``_(O.o)_/''
My vote still goes to doxygen. easy to use, lightweight and capable of a hell of a lot of languages. I did most of my editing in Sublime and it really was a pleasure.
I created a small snippet, so that adding the template comment took only 3 keystrokes and edited away :D
I really like the clean looks of the comments in the code. Sometimes liked this even better than the actual generated output (haha) ;)
So if you want to get proper documentation done, it'd recommend checking out doxygen !