I seem to recall wiping out ISKD Lib when I tested Java WebSphere - make sure it's backed up and delete it and see. Also - use some form of utility to find what are called "A68 files." There will be a ton of them left behind from uninstalled apps, and they tend to be "hidden;" TealMover allows me to see all of them and even make a category to search ONLY for a68's. Some utilities allow you to delete "all a68's," and then one you need recreate themselves - but I'd prefer to just eliminate old ones. They won't hurt you - but part of a neat cleanup is getting rid of them.
Also, you may have saved/unsaved prefs files for uninstalled apps too and I would consider it more important to clean those up. Do a search on here for "SysTool," 11k - which ONLY shows saved and unsaved prefs. Filez will do it too - I just like SysTool because it's easier to read and "deal with." It's freeware. You have to be careful looking for old saved prefs, as just because something says "unknown," doesn't mean it won't botch up program settings or unregister the product. Nothing too traumatic, but bothersome if you wipe out the wrong one. Uninstall Manager tends to take care of MOST saved/unsaved pref deletions (for proggies you load from now on) - but still misses a few here and there! That's why I prefer to do it "manually."
From now on, next time you load a program, look and see what saved/unsaved prefs it creates. They will be appended to the list (Palm doesn't alphabetize them, which drives me nuts). Make a note of them (start a database) - then you always know what you've got and what you can delete safely.
If you use the Palm uninstaller (stock), and then look for leftover saved/unsaved prefs and A68's it might have missed, you can be pretty assured of keeping your handheld pretty darn clean.
Recommendations:
SysTool, freeware, 11k
TomCatalog (allows you to search by creator id and other powerful stuff!, freeware, 39k
TealMover ($12, BEST, does a couple of things Filez won't) or Filez (freeware, very good also, does a couple of things TealMover won't!) - Both TOGETHER really rock. All 4 combined (3 free, 1 you pay for) would give you HUGE control over your file management.