If you backup your Preferences folder (as I do) you might notice that you are backing up VLC's cache files which are essentially trash and I can't imagine why anyone would have any need or desire to back them up, ever. It would certainly be nice if VLC stored its cache files in ~/Library/Caches which is the standard location for user cache files in OS X and has been for years.

Incidentally, the *actual* list of VLC's supported container file formats, video and audio formats is located at:
http://www.videolan.org/vlc/features.html