Hmm.. this is a tough one. But using the AA scale the following would be my rarest loose carts in my VCS collection:
Chase the Chuckwagon
However, I consider both of my Parker Bros. prototypes carts to be the most rare. Especially my WIP version of Star Wars: TAG.
I also have a decent condition Activision Checkers....with the foam insert. I keep that in the glass case as well. It was the last Activision title I really needed for the collection (Loose of course), and to find it with the foam insert still completely in tact was even better.