I'm quite liking Doxygen. Feels like Javadoc done right. I never liked having to manually feed files to javadoc, but Doxygen has a handy dandy UI to recursively feed it directories and files, and has all kinds of pattern matching and filtering at the file level. Cool.
There's even a MacOSX package that includes the command line and GUI wrapper.
The output isn't bad, either. I've only run it on a few apps now, and they are rather lacking in documentation (well, consistent documentation, anyway ;-).
One of the cooler things about Doxygen is the ability to have some (or all) of your documentation separate from the source code (or, by default, do it the same way Javadoc does). King's been complaining about the lack of header files in java, and this kinda sorta almost makes up for that. But not quite.
Check out the documentation for the EduSource ECL API.