The usual answer to fixing bouncing in the dock syndrome is reinstalling Java using the "Offline" standalone installer. If you're using Tiger I think that's this one Java 1.4.2 for Tiger (click on link), however if you're using Panther then try this one http://www.apple.com/downloads/macos...update142.html

BTW if it refuses to let you install, then double-click the harddrive icon, open the Library, open the Receipts folder, then find the file: Install java ???.pkg, delete it and try again. For Panther that's Java142Update2.pkg Sorry I don't have Tiger but a sample image for Panther is Receipts folder sample image which will give you an idea of what to do anyway. Who's going to buy Tiger for me lol

I don't know why it should have affected Java though. My guess would have been the protocol that allows LW & iTunes to share. I can't recall the name of it off-hand. Found it, Bonjour (Rendezvous)