In my opinion the 70's, 90's, and 2000's are all amazing
Crownsy - to respond to what you said about all movies in the 2000's being remakes and comic book movies, I will agree that we have seen an overload of those types of movies but that is just at the theater. If you look closely you'll find good movies.
For example (Alphabetic order from my library of movies I own):
1. Across the Universe (2007)
2. American Psycho (2000)
3. The Assassination of Jesse James (2007)
4. Atonement (2007)
5. The Aviator (2004)
6. Babel (2006)
7. Big Fish (2003)
8. Blood Diamond (2006)
9. Blow (2001)
10. Burn After Reading (2008)
11. Butterfly Effect (2004)
12. Children of Men (2006)
13. City of God (2002)
14. Collateral (2004)
15. Crash (2004)
16. Crouching Tiger, Hidden Dragon (2000)
17. The Curious Case of Benjamin Button (2008)
18. The Departed (2006)
19. Donnie Darko (2001)
20. Doubt (2008)
21. Eternal Sunshine of the Spotless Mind (2004)
22. Finding Nemo (2003)
23. The Fountain (2006)
24. Gangs of New York (2002)
25. Gone Baby Gone (2007)
26. Gran Torino (2008)
27. Hotel Rwanda (2003)
28. In Bruges (2008)
29. Into the Wild (2007)
30. Kill Bill vol. 1 (2003)
31. Kill Bill vol. 2 (2004)
32. The Kite Runner (2007)
33. Little Miss Sunshine (2006)
34. The Lookout (2007)
35. Lost in Translation (2003)
36. Memento (2000)
37. Milk (2008)
38. Munich (2005)
39. Mystic River (2003)
40. No Country For Old Men (2007)
41. O Brother, Where Art Thou? (2000)
42. Panic Room (2002)
43. Pan's Labyrinth (2006)
44. The Passion of the Christ (2004)
45. Phone Booth (2002)
46. The Pianist (2002)
47. The Prestige (2006)
48. The Reader (2008)
49. Requiem For a Dream (2000)
50. Revolutionary Road (2008)
51. Sin City (2005)
52. Slumdog Millionaire (2008)
53. There Will Be Blood (2007)
54. Traffic (2000)
55. The Wrestler (2008)
Not to mention movies I don't own yet such as Changeling, Inglourious Basterds, Frost/Nixon, and countless others...
With all of that said, I think I would still put the 90's on top, probably in the 2 spot as the second best decade because of movies like Pulp Fiction, Forrest Gump, The Shawshank Redemption, Titanic, Eyes Wide Shut, etc. I would put the 70's in 3rd with A Clockwork Orange, Woodstock, One Flew Over the Cuckoo's Nest, The Godfather I and II, Dirty Harry, Chinatown, Halloween, Alien, etc. I would definitely have to put the 2000's in first.
As far as the best single years...
2007 - Across the Universe, The Assassination of Jesse James, Atonement, Gone Baby Gone, Into The Wild, The Kite Runner, The Lookout, No Country For Old Men, There Will Be Blood.
2008 - Burn After Reading, The Curious Case of Benjamin Button, Doubt, Gran Torino, In Bruges, Milk, The Reader, Revolutionary Road, Slumdog Millionaire, The Wrestler.
1994 - Clerks, Forrest Gump, Pulp Fiction, The Shawshank Redemption.
1939 - Mr. Smith Goes to Washington, Gone With the Wind, The Wizard of Oz.