+1 for Sphinx. For me, it's crucial that code and documentation are kept closely together. As in, changes to the code and the related documentation go in the same commit. In my experience, that's the only way to keep them in sync. Sphinx works great in this scenario, can output the docs in many different formats, default HTML output has search built-in etc. It's cross-platform (although I've used it on Windows and Linux only, I'm pretty sure it works on Macs as well).
This is good stuff, too: http://johnmacfarlane.net/pandoc/