I use netbeans 3.2.1 with most of the source setup in the filesystems list (no problem -- all of the open source pieces have source available) then crank up tomcat with debugging turned on. You can do this remotely if firewalls permit by using tcp/port for debugging access.
I then attach to tomcat and set a breakpoint or two and hi-ho-de-merry-o-a-debugging-we-will-go Heitzso
