Difference between System.exit() and System.halt() method?

http://docs.oracle.com/javase/7/docs/api/java/lang/Runtime.html
public void halt(int status)
Forcibly terminates the currently running Java virtual machine. This method never returns normally.

This method should be used with extreme caution.
Unlike the exit method, this method does not cause shutdown hooks to be started and does not run uninvoked finalizers if finalization-on-exit has been enabled. If the shutdown sequence has already been initiated then this method does not wait for any running shutdown hooks or finalizers to finish their work.
public void exit(int status)
The virtual machine's shutdown sequence consists of two phases.
In the first phase all registered shutdown hooks, if any, are started in some unspecified order and allowed to run concurrently until they finish. In the second phase all uninvoked finalizers are run if finalization-on-exit has been enabled. Once this is done the virtual machine halts.

If this method is invoked after the virtual machine has begun its shutdown sequence then if shutdown hooks are being run this method will block indefinitely. If shutdown hooks have already been run and on-exit finalization has been enabled then this method halts the virtual machine with the given status code if the status is nonzero; otherwise, it blocks indefinitely.

Difference between Runtime.exit() and Runtime.halt()
You might have noticed so far that the difference between the two methods is that Runtime.exit() invokes the shutdown sequence of the underlying JVM whereas Runtime.halt() forcibly terminates the JVM process. So, Runtime.exit() causes the registered shutdown hooks to be executed and then also lets all the uninvoked finalizers to be executed before the JVM process shuts down whereas Runtime.halt() simply terminates the JVM process immediately and abruptly.
http://blog.joda.org/2014/02/exiting-jvm.html
Apparantly, System.exit(0) does not always stop the JVM!

System.exit(0) does not always stop the JVM. Runtime.getRuntime().halt(0) should always stop the JVM.

 public static void main(String... args) {
    Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() {
      @Override
      public void run() {
        System.out.println("Locking");
        synchronized (lock) {
          System.out.println("Locked");
        }
      }
    }));
    synchronized (lock) {
      System.out.println("Exiting");
      System.exit(0);
    }
  }

What does the code do?

1. Our code registers the shutdown hook
2. Our code acquires the lock
3. Our code prints "Exiting"
4. Our code calls System.exit(0)
5. System.exit(0) calls our shutdown hook
6. Our shutdown hook prints "Locking"
7. Our shutdown hook tries to acquire the lock
8. Deadlock - Code never exits

The main alternative is Runtime.getRuntime().halt(0), described as "Forcibly terminates the currently running Java virtual machine". This does not call shutdown hooks or exit finalizers, it just exits.

But what if you want to try and exit nicely first, and only halt if that fails?

   * Exits the JVM, trying to do it nicely, otherwise doing it nastily.
  public static void exit(final int status, long maxDelayMillis) {
    try {
      // setup a timer, so if nice exit fails, the nasty exit happens
      Timer timer = new Timer();
      timer.schedule(new TimerTask() {
        @Override
        public void run() {
          Runtime.getRuntime().halt(status);
        }
      }, maxDelayMillis);
      // try to exit nicely
      System.exit(status);
      
    } catch (Throwable ex) {
      // exit nastily if we have a problem
      Runtime.getRuntime().halt(status);
    } finally {
      // should never get here
      Runtime.getRuntime().halt(status);
    }
  }

Why runFinalizersOnExit is deprecated?
public static void runFinalizersOnExit(boolean value)
Deprecated. This method is inherently unsafe. It may result in finalizers being called on live objects while other threads are concurrently manipulating those objects, resulting in erratic behavior or deadlock.
Enable or disable finalization on exit; doing so specifies that the finalizers of all objects that have finalizers that have not yet been automatically invoked are to be run before the Java runtime exits. By default, finalization on exit is disabled.