This was an email I sent at work. I am blogging it because it took me way too long to find this information, and I don't want it to get lost.

Almost all of the official IBM documentation that you can find only tells you how to debug Websphere applications with the IBM "Distributed Debugger". I wanted to be able to use any standard JPDA-compliant tool. In my particular case, NetBeans.

Run startserver.bat like this:

startserver -debug -jdwpPort portnum

for instance:

startserver -debug -jdwpPort 99999

Then you can connect to this port and set breakpoints and watches using the your favorite IDE (which I am not going to explain how to use since I don't know what IDE you use or how to set it up).