I think my list has changed a bit in the last 4 years.
2. Blade Runner
3. Once Upon a Time in the West
4. The Searchers
5. American Graffiti
7. Raiders of the Lost Ark
8. The Empire Strikes Back
9. The Good, the Bad, and the Ugly
Honorable mentions: Bring Me the Head of Alfredo Garcia, Alice Doesn't Live Here Anymore, Citizen's Band, Alien, Immortal Beloved, The Fifth Element, Cool Hand Luke, and Rocky.
"The other versions will disappear. Even the 35 million tapes of Star Wars out there won’t last more than 30 or 40 years. A hundred years from now, the only version of the movie that anyone will remember will be the DVD version [of the Special Edition], and you’ll be able to project it on a 20’ by 40’ screen with perfect quality. I think it’s the director’s prerogative, not the studio’s to go back and reinvent a movie." - George Lucas