I am a huge fan of github, but browsing through the APIs, I don't feel like its the right format for hosting APIs. Its really hard to navigate and get a sense of what all the functions are and how they link together.
Agreed. Still - having letting your users send you pull-requests to the documentation is a good idea. My company apiary.io is building API documentation tools that take the open git repo benefits but generate a sensible-looking documentation.