We’ve been using Doxygen for a several projects:
flexible output options HTML, PDF, XML,
flexible markup,
pluggable language support.
http://www.stack.nl/~dimitri/doxygen/
Another nice thing, is it supports a fairly generic flavor of markdown as markup option; which is compatible with github/stash websites.
Active enough projects that bugs get fixed.
(I didn’t see any clear requirements at the beginning of the thread, so I’m highlighting what was important for our use)
Brian Kuhl