I have an installation of OpenSSO running on Glassfish. Everything is pretty much stock with as little configuration as possible to get the system working. I've started running into issues where the server will stop responding. It will accept requests but hang on the responses. After twenty minutes or so all of the requests complete, lightning fast, and everything is back to normal. Sadly, the logs don't show anything out of the ordinary that would be causing this.
What I am looking for is a general strategy. How would you go about diagnosing and resolving issues like these on Java Application servers?