Every time I update Quicktime on both Vista and XP, I lose file associations I made for VLC (my preferred player). I only keep QT around for the odd browser video, and would prefer to keep it without it surprising me every couple months by stealing file associations.
Buried in the advanced setup there is a checkbox to keep it from checking and reclaiming. Wish I could remember where though... I stopped using QuickTime a while back in an effort to simplify the media players that continually were sprouting on my PC... MediaPlayerClassic Home Cinema handles everything I need it to and then some.
I would highly suggest using Quicktime Alternative instead of the full blown Quicktime from Apple. It has plugins for all the major browsers and allows you to play Quicktime files in any video player. I have never had a problem with file associations using this software.