I've noticed problem with our app server. It seems that sometimes Tomcat keeps thread in status 'S' - (service) for a very long time. Although sometimes user's computer does not have active connection (session) in application which that Tomcat served, also even user's computer is 'shut down'.
If I look http://localhost/status I see something like this: ******* Stage Time B Sent B Recv Client VHost S 88751926 ms 0 KB 0 KB 10.32.65.17 'servername' 'GET.some.jsp' *******
Sometimes we called user and ask him to log in and logout from application, and usually it helps and thread disappeared from list, but sometimes it does not work.