For presentations we create a separate window for Alerts and open it on top of the PowerPoint or Impress window. Can't we do the same for VLC/Phonon?
I'm not sure we should be classifying this as a wishlist. A year ago alerts worked throughout (yes I know VLC didn't exist then) but now it doesn't work throughout.
What type of media and which player were you using?
When Os are you running?