Thanks everyone and this forum.
rkapsi ponted out the problem and RealityX showed the way to the solution in his thread - HOWTO - Solve the problem with Java and LimeWire (HOWTO - Solve the problem with Java and LimeWire
by disabling the Java alternatives in Fedora Core 3 and using the j2se sdk to install it properly. In addition to the above post, I changed the /usr/bin/java softlink to point back to the real java instead of /etc/alternatives/java.
Limewire is now operational again for me.