Similar* to the books lists here in the past, the title of the anime applies not just to one series, OVA or movie, but exists as a category, where applicable.
1. Cowboy Bebop
2. FLCL
3. Ghost in the Shell
3. Samurai Champloo
4. Akira
5. Spirited Away
6. Tekhnolyze
7. Bleach
8. Vampire Hunter D
9. Hellsing
10. Witch Hunter Robin
11. Elfen Lied
12. Soul Eater
13. Kamichu
14. Death Note
15. Darker than Black
16. Appleseed
17. Princess Mononoke
18. Ah! My Goddess
19. Durarara
20. High School of the Dead
21. Ninja Scroll
22. Black Lagoon
23. Rurouni Kenshin
24. Clannad
25. Canaan
26. Frozen
27. Level E
28. Howl's Moving Castle
29. Escaflowne
30. Gosick
31. Ergo Proxy
32. Sayonara Zetsubou Sensei
33. Mononoke (Ayakashi)
34. Nichijou
35. Steins;Gate
36. Pale Coccoon
37. Genius Party
38. Usagi Drop
39. Battleship Yamamoto
40. Haruhi Suzumiya
41. Steamboy
42. Honey and Clover
43. Potemayo
44. School Days
45. Gintama
46. Dead Man Wonderland
47. Evangelion
48. Love Hina
49. Togainu no Chi
50. Full Metal Alchemist
51. Monster
52. Wizards
53. Wolf's Rain
54. Tekkon Kincrete
55. Rainbow
56. Perfect Blue
57. Godfathers of Tokyo
58. Black Butler
59. Trinity Blood
60. Wicked City
61. Dirty Pair
62. Panty and Stocking
63. Berserk
64. .hack//
65. Read or Die
66. Mind Game
67. Golgo 13
68. Scryed
69. Strike Witches
70. Detective Conan
71. Lupin III
72. Xam'd
73. Planetes
74. Gallery Fake
75. Galaxy Express
76. Final Fantasy
77. The Animatrix
78. Summer Storm! Open for Business
79. Akahori Gedou Hour Rabuge
80. When the Seagulls Cry
81. Bakuman
82. Michiko and Hatchin
83. Natsume's Book of Friends
84. Yondemasuyo, Azazel-san
85. Moshidora
86. We Still Don't Know the Name of the Flower We Saw That Day
87. Freedom (really this is like #1, and #86 is like #2, etc.)
88. The Girl Who Leapt Through Time
89. Paprika
90. Kobato
91. Memories
92. 5 Centimeters Per Second
93. Spriggan
94. Laputa
95. Metropolis
96. My Neighbor Totoro
97. Only Yesterday
98. Cromarty High School
99. Paranoia Agent (almost does not make this list)
100. Blue Exorcist
I keep thinking that some of the really great stuff is late on the list. This is just personal opinion. I refuse to list a very large number of anime because THEY SUCKED [Intentionally left off: One Piece, Naruto, Dragonball, Samurai Seven, Basilisk, Gunslinger Girl, Sailor Moon, Card Captor Sakura, Inuyasha, Trigun, Gundam, Fate/Stay Night, and many others. I'd be willing to take these apart episode by episode to prove that my intense dislike was not from a failure to let a series develop] but just because it isn't here doesn't mean it's not good. I may not remember it right now. I may even have not seen it, although I try to remedy that when good things circulate...
* [On the books lists only one book was listed by each author, although every book by that author was usually fantastic]