Thanx for the reply, unfortunately that does not help me.
As far as I understand, "orderToFront" only brings the NativeWindow infront of other NativeWindows inside your application. It does not put my NativeWindow (in this case my air app) above all the other windows / apps that is currently running on your pc. Here is a good article that explains the z order of chromeless windows: http://www.adobe.com/devnet/air/flex/quickstart/articles/controlling_display_order_windows .html
alwaysInFront is set to true, but this helps to put air app above other windows running on your pc. eg. if You have My computer and my air app next to each other, the air app is above, my computer is always behind. So this is doing the trick for all other applications, even when you have vlc full screen. This does not work for Windows Media Center. If you open Windows Media Center in full screen, you will see, it almost looks like it goes into a 'mode' that looks similar to when you open a game (takes control off your full screen and block your mouse from leaving the active screen)
I created a qt application that can display messages in your systemtray, but even this did not work yet.
Thanx again for the reply.