I just realized from an article in CACM that Doxygen works with Java (and several other languages) too. But Java has already the Javadoc tool. Can someone explain what are the pros and cons of either approach? Are they mutually exclusive? Is there a Maven plugin for Doxygen?
Doxygen has a number of features that JavaDoc does not offer, e.g. the class diagrams for the hierarchies and the cooperation context, more summary pages, optional source-code browsing (cross-linked with the documentation), additional tag support such as @todo on a separate page and it can generate output in TeX and PDF format.It also allows a lot of visual customization.
Since Doxygen supports the standard JavaDoc tags you can run Doxygen on any source code with JavaDoc comments on it. It often can even make sense to run on source code without JavaDoc since the diagrams and source code browsing can help understanding code even without the documentation. And since the JavaDoc tool ignores unknown tags you can even use additional Doxygen tags without breaking JavaDoc generation.
Having said all this I must admit that I haven't used Doxygen for a long time. I tend to rely heavily on my IDE nowadays to provide the same visualization and I usually don't read JavaDoc as HTML pages but import the source files into my IDE so it can generate JavaDoc flyouts and I can jump to the definitions. That's even more powerful than what Doxygen has to offer. If you want to have documentation outside the IDE and are happy to run non-Java tooling then Doxygen is worth a try since it doesn't require any change to your Java code.