To free up space, I used Red Hat Package Manager (RPM) and reviewed all of the packages installed on the server, looking for ones I don't need such as Gnome and X11 windowing packages and non-English support.
A few observations:
Check out http://jpackage.org/
Looks interesting. Do you know if it tracks Java class library dependencies?
I believe Mandrake has the install and remove feature you're looking for. You can browse packages and updates by caregories, and I *think* you can install them in groups as well. Even if you can, you can at least view things a lot easier. The newest version of Mandrake just hit the ftp servers, too (9.2).