doxygen => fu** javadoc
I am just looking at some tool for documenting a little C++ project I am doing. (A C++ wrapper for curl will be up shortly). And I had a look at doxgen. And it is brilliant. There is a little GUI tool called doxywizard that will generate the config file that you then can feed into doxygen. It is possible to create HTML, Latex, man, rtf and XML with little in line graphics and so on(Call graphs, Class diagrams, ...). I am loving it. Having used javadoc previously this is so much nicer and more configurable. And it can format the source code nicely so clicking on the function name can take you to the actual code, what I consider brilliant for open source projects. So have a look at it especially if you are using JavaDoc.