Top 10 of the '60s and '80s, prone to rapid change at any time.
1960s
1. The Graduate
2. 8 1/2
3. Belle du jour
4. Butch Cassidy and the Sundance Kid
5. Midnight Cowboy (I just rewatched this a few days ago. Wow. Those filmmakers were on drugs. Still a great movie)
6. Blow-up
7. Repulsion
8. The Apartment
9. To Kill a Mockingbird
10. La dolce vita
1980s
1. Amadeus
2. Raging Bull
3. Do the Right Thing
4. Tootsie
5. Hannah and Her Sisters
6. When Harry Met Sally...
7. Wings of Desire
8. The King of Comedy
9. The Shining
10. The Princess Bride
Let's all note that according to AFI, all of those movies except Raging Bull and Tootsie are apparently inferior to Sophie's Choice.
