Debugging a remote application from Eclipse.
When you are debugging a remote application, or one that is not running within your IDE, you start the application with, something like:
java -agentlib:jdwp=transport=dt_socket, address=8000,server=y,suspend=n SomeClass
See http://publib.boulder.ibm.com/infocenter/iseries/v5r4/index.jsp?topic=/rzaha/jpdebuga.htm
Then in Eclipse, you go to the Debug Configurations, in the Remote Java Application section and enter the corresponding information there. Then start a session.
I'm going through this quickly because I think most already know about it.
There are a couple of other things: 1) the code on the other computer has to be compiled to have debugging information, and 2) you need to make sure your firewall hasn't blocked the port.
Also, don't forget the JConsole utility. It will let you do a lot of monitoring of an application, such as determining how memory is used.