Update for 1.4_00_01 -- if you bypassed Bukkit, you will most likely break.

src/main/java/org/bukkit/craftbukkit/util/ServerShutdownThread.java

@@ -12,6 +12,6 @@ public class ServerShutdownThread extends Thread {
 
     @Override
     public void run() {
-        server.g();
+        server.stop();
     }
 }