It should. I vaguely recall some problem with the iTunes prefs in the past. Might be worth trashing those first just in case.

You could also just trash the LW prefs (System Folder->Preferences->.limewire->limewire.props. That one has your settings. The fileurns.cache contains the hash of your shared files, and if you are sharing a lot, it's the one that takes so long to rebuild when starting up. If you only have a few files and don't mind starting from scratch, just trash the whole .limewire folder.

For a simple uninstall, run the uninstaller in the LW folder. You can run sherlock to find any other LW files that don't get uninstalled. The installer also writes a file called .com.zerog.registry.xml. I like to delete it, but I don't know what it does.

You can leave your incomplete folder as is (the downloads.dat file in it remembers what it can to resume incomplete files), but if you don't mind losing any incomplete downloads, delete that folder too to really restore your HD.

Hope trashing the iTunes prefs works, but going through the uninstall process can be good to know.