Several users have emailed about this: If you have upgraded to Snow Leopard and are using Join Together you will need to install QuickTime Player 7. And be sure to get the latest version of Join Together.
QuickTime Player 7 is in "Optional Installs" on your Leopard Install disc. Open this folder, run "Optional Installs.mkpg", and make sure "QuickTime Player 7" is checked.
After installing QTP7 (or if it is already installed), you can find it in /Applications/Utilities/. Activate it and run it long enough for it to establish a full launch, and then quit it. This will be enough activity for its preferences file to be created, which Join Together needs to locate.