After installing QuickTime 6.1, the QuickTime plug in quit working for me in Safari. I found that I had an older QuickTime plug-in in ~/Library -> Internet Plug-Ins (in my home directory), and the new one in /Library/Internet Plug-Ins. I removed the one in my home directory, and the new 6.1 plug-in is now recognized and QuickTime now works in Safari.
Mac OS X Hints
http://hints.macworld.com/article.php?story=2003012306493276