I seem to recall these things being contained in their own special type of track, in which case you ought to able to disable it in the "Show Movie Properties" window (QT7, under the Window menu), or the "Enable Tracks..." window (QT6 and below, under the Edit menu). That would have to be done on a movie-by-movie basis, though. And I'm going strictly from memory, as I don't have any example movies on hand.
A more heavy-handed approach would be to disable the ability for any application to launch an URL. You can effectively do this by going to Safari's preferences and changing the "Default web browser" to the Dock ("/System/Library/CoreServices/Dock.app"). Then all URL requests from apps like QTP will be sent to the Dock, which will neatly ignore them. The problem is, that will also break links in, say, your email client or TextEdit.
Sirstaunch: Are you absolutely sure VLC and MPlayer support this feature? Has anyone actually tested it? They don't use QT to play QT movies, so it'd stand to reason if they didn't.
