I got the chance to play with debugging a running WebObjects app today, with the added fun of having a roomful of 20 users of the app taking turns to mention "did you know that [X|Y|Z] isn't working?"
Long story short, if you need to get the status of threads of a running WebObjects app, jdb provides some great tools. I have only scratched the surface of it, thanks entirely to the great intro document by Andrew Lindesay. (Andrew recently moved his website to .Mac from some New Zealand host, so I'm linking to help throw some Google Juice his way so others can find his article)
I've put a wikified crib sheet together to make it easier to get set up.