I've always wanted to see the original version of Galaxy Quest. It had more violent scenes, more swearing (some obvious dubs can still be seen in the movie) and was just darker. It probably would have gotten an R rating, and the test screening audience wanted to change all that.
The original 4-hour cut of Blue Velvet. Too bad the two hours of deleted scenes still cannot be found.
I would like to see Little Shop Of Horrors with the orignal ending attached. This one has the plant eating Audrey and Seymour, and conquering the world, Godzilla-style. The preview audience didn't like it, even though the ending is the same as the original Broadway-version. There are rumors that David Geffen is re-releasing the movie, with the original ending intact. I hope it happens.