To enable Java remote debugging on the Sun JVM, use the command line:
java ... -Xdebug
-Xrunjdwp:server=y,transport=dt_socket,address=6666,suspend=n
In Eclipse, go to the Debug launch configuration screen and create a new "Remote Java Application" configuration that uses the address specified in the -Xrunjdwp argument. Once you are finished debugging, click on the 'disconnect' button in the Debug view.