This might be obvious to many, but it wasn't to me. I wasn't able to get Flash movies from certain sites to work in Safari until I unchecked the Flash box in the QuickTime System Preferences panel -- click on the MIME Settings button, then look in the Miscellaneous section and uncheck Flash.
Some talk on this subject can also be found on the Apple Discussions site; search on "quicktime flash safari" to see a thread on the issue.
[robg adds: An older hint discusses a different (but related?) issue with Mozilla and Flash movies.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20031020204245774