Best Way to Gracefully Shutdown a Java Command Line Program

you can try something like this:

Runtime.getRuntime().addShutdownHook(new Thread() {
    public void run() { /*
       my shutdown code here
    */ }
 });

edit:

the shutdown hook will not perform the shutting down of the app. instead, it gives the developer a way to perform any clean-up that he/she wishes at shutdown.

from the JavaDoc for Runtime (a good read if you are planning to use this method):

A shutdown hook is simply an initialized but unstarted thread. When the virtual machine begins its shutdown sequence it will start all registered shutdown hooks in some unspecified order and let them run concurrently. When all the hooks have finished it will then run all uninvoked finalizers if finalization-on-exit has been enabled. Finally, the virtual machine will halt. …