Using the iTunes control keys for VLC
Running OS X Lion 10.7.2, VLC 1.1.12 -- this desired "proper" functionality suddenly appeared, perhaps as a result of the update from 10.7.1->10.7.2 the other day. Or perhaps as the result of a VLC update. 

Control of VLC and iTunes via Apple Keyboard hotkeys is now decoupled. The active player responds to hotkey keypress.