I've always had the same desire, POD just doesn't do enough for me and I've always been jealous of the clean way java does it with javadoc. We just ended up writing our own script to do this, maybe I'll get it posted so others can use it.

I've heard somewhere out there their is a script that will allow you to use doxygen with perl, I don't remember the link but I think you can find it from the doxygen web site.

Another tool you might want to look at is pdoc.