The compilations probably shouldn't be counted, but since it was just for fun, I decided it wouldn't hurt anything. People can throw them out if they want. As a side note, all of the votes for The Godfather Part III came from people saying "The Godfather trilogy".
It's always strange for movies that are essentially multiple parts of a longer story. The Wachowski brothers have already said that the two upcoming Matrix sequels are really two parts of one movie. And if I really wanted to push, I'd throw the 100-hour movie called Babylon 5 on there. :-)
With that, I think I might start on a few more polls soon. This one was fun and educational.