You have to delete it completely. Even it's preferences. Run a search for Limewire in the Finder and delete everything.
You can also try uninstalling, dlding and reinstalling Java. It could be that with the upgrade came in a new Java that got corrupted in the dld (even though I'm pretty sure that Jaguar and Panther use the same Java)

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iMac G4 OSX 10.3.9
RAM 256MB
LW 4.10.5 Basic
ADSL anything from 3 to 8Mbps/around 1024kbps

"Raise your can of Beer on high
And seal your fate forever
Our best years have passed us by
The Golden Age Of Leather"
-Blue Öyster Cult-