Doxygen is as everybody knows, the de-facto standard for generating API documentation from source code comments. But it is also pretty great for generating user documentation, as is apparent from the Doxygen documentation itself. And with the really good Markdown support in recent versions, it is no longer necessary to write the documentation in “fake” code. Just plain Markdown works great.
There are a few gotchas, though, as I discovered when trying to generate a QT Assistant help file for the application I’m currently working on.