Sometimes we can shutdown a tomcat instance properly, sometimes we need to kill the java process.
This is because there are "user" threads running inside the JVM.
These threads are called "user" when there are created using new Thread() or new TImer() but they can be turned into daemon threads using:

Thread t = new Thread();
t.setDaemon(true);
...
new Timer(true);

For more information see:
http://java.sun.com/j2se/1.4.2/docs/api/java/lang/Thread.html#setDaemon(boolean)