doxygen does give you some ability to customize the output. From the doxygen docs:

Since version 1.2.18, Doxygen can generate a new output format we have called the "Perl Module output format". It has been designed as an intermediate format that can be used to generate new and customized output without having to modify the Doxygen source. Therefore, its purpose is similar to the XML output format that can be also generated by Doxygen. The XML output format is more standard, but the Perl Module output format is possibly simpler and easier to use.

Actually, the idea with XSLT is interesting - since doxygen can generate preparsed XML, I should be able to create some nice HTML styles through XSLT and possibly some further postprocessing. I have to look into that.

Thanks for the suggestions everybody. At least I now see a workable alternative approach, I'll have to see how we can minimize the efforts required. I'd really like to get professional level source code documentation using an OSS approach, beyond doxygen & co. Heh, what a perfect opportunity to delegate some annoying XML work to another team member [grin]

There's also Synopsis.

The whole thing is Python, and written with a pretty general design. (Parsers create ASTs, Filters traverse them)