That's rather an issue of reading the ps/top output. First of all, each Java thread in your ps-output shows the memory, the whole JavaVM uses up. ps is unable to show the memory usage of a single thread. So if a java thread is using up 60000k or something, that will mean that the whole JavaVM is using that memory and not the single thread.

Top will never show your memory empty or even nearly empty, by the way, since linux is using "free" memory for the purpose of caching.

You also don't have to reboot your computer. "killall java" usually just works fine, although your computer may have a hard time reacting, if your cpu time is really used up.

The number of threads (and thus also memory usage) is currently still a problem LimeWire has, - LimeWire needs two threads per connection, so if you are an Ultrapeer with up to 81 connections, you easily hit the bottom line. However I know, the LimeWire developers are working on that issue. This will take some time, they will have to restructure the way LimeWire handles the connections completely. LimeWire was initially not designed to handle such a number of connections.