My guesses:

Your application has bad sync locking between some threads, which is
causing one thread to block the others.

Your application has bad database access code, which allows one thread
to block others while waiting on the DB.

Your application is disk bound, and the single long process is hashing
the disk drives so much that is has dragged down the rest of the OS,
making it very slow to respond to the IO request of the other, small

You haven't configured the GC  well - however, I would expect this to
cause sporadic  problems, rather than continuous ones.

There are numerous JVM tools out there to help you with all of these
issues - from the simple garbage collection monitor that comes with
java (JConsole
 to full blown tools like JProfiler (which last I checked, had a free

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