Ask HN: How do you document your applications?

I'm wondering what are others using to store documentation of their (non-public) services. Github wiki looks nice, but including charts/diagrams is a pain. It has the advantage of keeping docs close to the code, but searching wikis does not work.

Confluence kind of works (and has gliffy integration!), but its search is also terrible.

I'm referring to documents like: architecture overview, what is it and how it works, user guide, but a place for javadoc/godoc would be nice as well.

What works best for you?