Whenever I uninstall LimeWire from my computer, a bunch of files with a "jar" extension get left behind. I try to delete them, but it keeps saying another program is using them, but I have no idea what program this could be, and they are really taking up space that I need. Any ideas how I can get rid of them?

How are you uninstalling LW? If you're doing it via Add/Remove programs then that can cause problems!!
The correct way to uninstall is start > all programs > LW & use the uninstall option there, or C:\Program Files\Limewire\uninstall

Use your computer's search to look for all files & folders with limewire in the name. If you can't delete them, reboot into safe mode & then try. If they still won't delete, try one of the tools here (I've used both Unlocker & DelinvFile).
http://www.gnutellaforums.com/174735-post2.html