I\'m experiencing a strange but severe problem running several (about 15) instances of a Java EE-ish web applications (Hibernate 4+Spring+Quartz+JSF+Facelets+Richfaces) on T
What happens after your app is performing slow for a while, does it get back to performing well? If so then I would check if there is any activity that is not related to your app taking place at this time. Something like an antivirus scan or a system/db backup.
If not then I would suggest running it with a profiler (JProfiler, yourkit, etc.) this tools can point you to your hotspots very easily.