I was recently adding some new Mail Rules to Apple Mail, and noticed all my rules that triggered an AppleScript were no longer associated with the correct scripts. Turns out the new version of Mail in 10.8 has a special folder specifically for scripts used in Apple Mail.
To fix, just open up any mail rule, click on the drop-down menu item “Open in Finder” to reveal the special scripts folder for Apple Mail, and drag your scripts into this folder. Existing rules seemed to have updated themselves to refer to the proper script once the script files were in that folder, but I still went ahead and checked each one manually to be sure.
Would have been nice if Apple alerted you to the change.
Update: this tip is now posted at Mac OS X Hints.