Recognizing that you're probably just shilling for your own product ... We use http://sphinx-doc.org/ http://sphinx-doc.org/ and author in ReStructuredText wit

Recognizing that you're probably just shilling for your own product ... We use http://sphinx-doc.org/ http://sphinx-doc.org/ and author in ReStructuredText with some extensions. From that, we output HTML, PDF and ePub. There are some issues with the ePub (they display fine, but don't validate), so it looks like sometime soon, I'll be hacking on Sphinx to fix some of the bugs in the epub generation. I couldn't really be happier with this system.