VLC bears no relation to QuickTime; it uses its own set of codecs and file parsers. So you should expect differences in the way QuickTime and VLC handle certain files.
However, if you have MPEGs that play sound in VLC but not QT, I can almost guarantee you that they're not real MPEGs. Windows users often misname any ol' movie file ".mpg", even if they're really mov, wmv, avi, etc. It's probably really an avi. If I'm wrong and it is in fact an MPEG, it means that it's somewhat corrupt. QuickTime is notoriously non-error-tolerant, whereas VLC is
very error-tolerant.
Like ElDiablo said, you probably need Divx. You might also need to download
the Ogg Vorbis codec and
AC3 Codec. Both are free.