If you will be using the file for web, check out this tutorial. You will have to create an automatic HREF Track:
http://www.apple.com/quicktime/tutor...reftracks.html
If, on the other hand, you will be using the files off the web, it gets a little complicated and I'll be glad to provide conversion service for minimum of 500 movies. The popups will appear irrelevant of whether the movie is played from the website or standalone QuickTime player.
