1SO is wrong as usual.
Anyway, my Top 5:
1. Apocalypse Now: Redux - There is literally one scene I'd cut out. One. And it's a Redux scene. The love scene in the French Plantation sequence always feels out of place, and not in a good way.
2. Amadeus: Director's Cut - A tough one. I guess I do have a bit of a problem, with, well, actually. Nope. Nothing about it I don't love.
3. The Apartment - Here's another one where I just can't think of anything I don't love. I know some people complain about the Jewish stereotypes, but I find them totally funny.
4. Vertigo - There's one problem I have with this film. In the first half, there is a bit of drag. Some scenes in the middle could have been slightly tightened to both enhance the romance AND the tension. But it's a really small issue.
5. Once Upon a Time in the West - I know it's unavoidable, but I don't like the dubbing. I find it distracting at many points.