Here it is, in no particular order! I had a hard time making this list because there are so many great films that were made in the 2000's! A Top 50 will not do them justice, so I limited the films to those that resonated with me at some point, and are at the top of my mind when I had to recall some. Reason being top of the mind is because if you recall a good film easily, then it has to have some meaning, some value to it! Bear in mind that this is my opinion, feel free to agree or disagree at my choices.
I had to cheat the list at some point, especially the trilogies, because they will eat up space on the list if I spread them out.
The list encompasses many geographic regions just for fairness' sake, and don't be alarmed that your favorite Hollywood film did not make the cut. Just because I did not include your favorite CG-heavy Hollywood film, I ask you to strip the CG, strip the effects and watch it again.
And by no means is this a definitive list! Also, if you have a film that ranks in your best of but not in mine, it might be because I haven't seen it yet. hehe, e.g. Moulin Rouge and Inglorious Basterds
Had to verify some of the release dates just to be sure (I almost put in American History X and American Beauty but found out it was released 1998 and 1999, respectively). And I was tempted to include re-releases but it's unfair hehe.
Again, in no particular order (those in bold are my top favorites):
1. Y Tu Mama Tambien (2001) - leave it to Alfonso Cuaron to direct a wonderful coming-of-age road film on friendship, sexuality and love.
2. Eternal Sunshine of the Spotless Mind (2004) - You just have to hand it to Gondry + Kaufman. Surreal kung surreal. With wonderful performances by Kate Winslet and Jim Carrey.
3. Le fabuleux destin d'Amelie Poulain (2001)
4. Paris, je t'aime (2006)
5. Persepolis (2007) - animated coming-of-age film of a girl during the Islamic Revolution. Political, whimsical, funny and poignant.
6. Star Trek (2009)
7. District 9 (2009)
8. The Incredibles (2004)
9. Let the Right One In (2008) - I love this film because it's quiet, not just in terms of audio but in the emptiness of the scenes' framing, yet what it lacks visually, more than makes it up for its unconventional love story of its protagonists.
10.Chicago (2002)
11. The Descent (2005) - My best horror film of the decade! Feminism, cave trekking, and literal darkness.
12. The Dark Knight (2009)
13. City of God (2002)
14. The Lord of the Rings Trilogy (2001, 2002, 2003)
15. Lost In Translation (2003)
16. No Country For Old Men (2007)
17. Wall-E (2008)
18.Up (2009) - There's just something painfully striking for me about letting go and starting anew.
19. Spirited Away (2001) - Hayao Miyazaki's strongest work of the decade; visually fantastic, appealing to all ages.
20. Pan's Labyrinth (2006) - Masterful work by Del Toro. Opens like a fairy tale, reveals a painful reality, and ends tragically.
21. Gladiator (2000)
22. The Bourne Trilogy (2002, 2004, 2007)
23. Amores Perros (2000)
24. Crash (2004)
25. Before Sunset (2004)
26. Children of Men (2006) - I love films dealing with post-apocalyptic scenarios, especially when well-written, unconventional, and uses mind-blowing one shot cinematography (yes, even when digitally stitched). And especially when it's directed by Cuaron.
27. Kill Bill vol. 1 & 2 (2003, 2004)
28. Punch-Drunk Love (2002)
29. A.I. (2001)
30. Crouching Tiger Hidden Dragon (2000)
31. Zodiac (2007)
32. Adaptation (2002)
33. Juno (2007)
34. Hable con Ella (2002)
35. Superbad (2007)
36. 28 Days Later (2002) - Correct me if I'm wrong, but I think this is the first film to show us rabid zombies and from where the iconic game Left 4 Dead gets its inspiration. Why I think this is great: independent, low budget, shot on a DV camera (Canon XL1), and features empty scenes of an eternally busy London.
37. Donnie Darko (2001)
38. Battle Royale (2000)
39. Antichrist (2009)
40. Hero (2002)
41. Ratatouille (2007)
42. The Darjeeling Limited (2007)
43. Harry Potter and the Prisoner of Azkaban (2004)
44. Jeux d'enfants (2003)
45. Grizzly Man (2005)
46. The Last King of Scotland (2006)
47. Once (2006)
48. Traffic (2000)
49. Perfume: The Story of a Murderer (2006)
50. The Royal Tenenbaums (2001)