This happens to me several times a day. I'll quit an app, the window will close, but the app won't finish shutting down. It stays open in the dock, and right clicking and force quit show not responding. Force quit won't work. I can't shut the app down. Starting any other app when this happens causes that app to behave in exactly the same way: the icon opens in the dock, but the app is non-responsive and can't be forced to quit.
Can't access terminal when this happens, because it locks up just like all the apps. While I haven't tried to open every app, I think any app I try to open when this is happening will lock up. If I relaunch Finder, it too locks up and then the only thing left is to hold down the power button for a hard reboot.
Any app that is running while this is happening will continue to run normally unless I try to shut it down.
Repairing disk permissions has no effect. I also did a time machine and a full restore on a brand new MbP - and sure enough, after restore, the new MbP suffers form the same problem. Creating a new user has no effect.
MacBook Pro 15" AG 2.53ghz i5 cpu 8gb RAM 500gb HD (over 200gb free)