I really like using iodocs by Mashery, it's pretty simple (put all of your API calls into a single JSON file) and it allows you to quickly do example calls with different query parameters that your users can test out right on the documentation. Klout uses it now too, I believe.
It's also open source, which makes developer me happy. The only thing I wish they would update is allowing JSON to be sent in the request body, which there seems to be an open pull request for on GitHub: