Hoss - have you tried XDoclet?
When i first started experimenting with this idea, i assumed a javadoc doclet would make the most sense .. then i tried making one, and i gave up because it has, by far, the worst "API" I've ever used in my life (caveat: i'm refering solely to Java APIs when i make that statements). So then i started looking at existing third party javadoc doclets, hoping to find a nice one that would already extract all of the useful info into XML so i could use XSLT (there was one, but it's really old and couldn't handle some pretty basic stuff) and then i started looking at other technologies. After experimenting with many of them, I went back and revisited the javadoc doclet approach: came to grips with the cluster f*ck of an API, ignoring the parts of it that were truly abhorent, and using only the core pieces that were really needed (my first attempt was trying to subclass the standard doclet to acutally incorperate the new pages into the existing javadoc navigation) which lead me to the current patch.
XDoclet, XDoclet2, and QDox (the java parser that XDoclet2 uses) were all on that list of other technologies, i don't remember specifically why i decided not to go with them, but one of the broader issues with most alternate solutions was that since they used good APIs for doing things, they couldn't be hooked into normal javadocs – one of my goals is to try and get to the point where developers write one "doc" for each plugin, it lives in the code and is displayed both in the javadocs for the plugin, as well as in the scaled down "user" docs that this would generated. generating "user" documentation about a plugin using something like XDoclet probably would have been easy – but to get the same information included in the "developer" javadocs would require just as much orthoginal Taglet work as i'm doing now – and simple things like
tags in the body of a javadoc comment wouldn't work automaticly with XDoclet2 (at least: not as far as i can tell)
XDoclet2 certianly seems like the best way to auto generate information from java code but for processing javadoc comments, i (unfortunately) couldn't find many solutions better then javadoc doclets and taglets.