Top 50 Anime of the 21st Century, According to NicoNico

The ranking, based on a composite of “title/production/story power,” “character power” and “anime music power”:
1. Bakemonogatari
2. Clannad
3. To Aru Kagaku no Railgun
4. AIR
5. Angel Beats!
6. Haruhi
7. Mahou Shoujo Madoka Magica
8. Ano Hi Mita Hana
9. Toradora!
10. K-ON!
11. To Aru Majutsu no Index
12. FMA
13. Lucky Star
14. Code Geass
15. Steins;Gate
16. Toki wo Kakeru Shoujo
17. Higurashi no Naku Koro ni
18. Macross F
19. Natsume’s Book of Friends
20. Mahou Shoujo Lyrical Nanoha
21. Ore no Imouto
22. Gintama
23. Hayate no Gotoku
24. Minamike
25. Full Metal Panic
26. Eureka Seven
27. Shakugan no Shana
28. Spirited Away
29. Grave of the Fireflies
30. Sora no Otoshimono
31. Working!!
32. Gurren Lagann
33. Ghost in the Shell
34. Fate stay/night
35. Infinite Stratos
36. Rozen Maiden
37. Amagami SS
38. One Piece
39. Seitokai no Ichizon
40. Aria
41. Garei Zero
42. Gundam Seed
43. Durarara!!
44. Naruto
45. Zero no Tsukaima
46. Milky Holmes
47. Hanasaku Iroha
48. Tiger & Bunny
49. Shinryaku! Ika Musume
50. Sousei no Aquarion

 Source: Sankaku Complex

 Jayce's notes: Interesting list, not surprised at the placings for top 10 either, considering the new trends these days.