Tsutaya and Newtype(Japan) magazine recently did a joint top 100 anime poll with "fans nationwide."
1) Mobile Suit Gundam SEED and Mobile Suit Gundam SEED Destiny
2) Neon Genesis Evangelion
3) Full Metal Alchemist
4) Cowboy Bebop
5) One Piece
6) Kyo Kara Maou
7) Mobile Suit Gundam
8) Card Captor Sakura
9) Fate/stay night
10) Akira
11) Dragonball Z
12) The Melancholy Of Haruhi Suzumiya
13) Detective Conan
14) Martian Successor Nadesico
15) Castle In The Sky: Laputa
16) Ghost In The Shell
17) Soukyuu No Fafner
18) Saint Seiya
19) Nausicaä Of The Valley Of The Wind
20) Hunter x Hunter
21) Keroro Gunsou
22) Bleach
23) Lupin III: The Castle of Cagliostro
24) Mobile Police Patlabor
25) Full Metal Panic
26) Initial D
27) Mobile Suit Zeta Gundam
28) Air
29) King Of Braves GaoGaiGar
30) Urusei Yatsura
31) Fist Of The North Star
32) Eureka 7
33) Konjiki No Gashbell (Zatch Bell)
34) Howl's Moving Castle
35) Pokemon
36) Naruto
37) Top Wo Nerae 2
38) .hack
39) RahXephon
40) Slayers
41) Lupin III
42) Future Boy Conan
43) Tenchi Muyo!
44) Yu Yu Hakusho
45) Ranma 1/2
46) Maria-sama Ga Miteru
47) New Mobile Report Gundam W
48) Scryed
49) Infinite Ryvius
50) Captain Tsubasa
51) Turn A Gundam
52) Nadia: Secret of Blue Water
53) Blood+
54) Ashita No Joe
55) The Prince Of Tennis
56) Futari Wa Precure: Max Heart
57) Space Runaway Ideon
58) Kiddy Grade
59) Super Dimensional Fortress Macross
60) Honey And Clover
61) Revolutionary Girl Utena
62) Mobile Suit Gundam ZZ
63) Mahou Shoujo Lyrical Nanoha
64) Sailor Moon
65) Mobile Suit Gundam 08th MS Team
66) Space Cruiser Yamato
67) Oh My Goddess!
68) Black Jack
69) Rozen Maiden
70) Duel Monsters
71) Galaxy Express 999
72) Mobile Suit V Gundam
73) Saiyuki
74) Aura Battler Dunbine
75) Doraemon
76) Onegai Teacher
77) After War Gundam X
78) Crayon Shin-Chan
79) Demonbane
80) Touch
81) Ojamajo Doremi
82) Mobile Suit Gundam F91
83) Hellsing
84) Slam Dunk
85) Grave Of The Fireflies
86) Giant Robot: The Day The Earth Stood Still
87) Trinity Blood
88) Paranoia Agent
89) Heavy Metal L-Gaim
90) Steamboy
91) Mushishi
92) My Neighbor Totoro
93) Inuyasha
94) Appleseed
95) Mai-Otome
96) Round Vernian Vifam
97) Millennium Actress
98) Tohai Densetsu Akagi
99) Nurse Witch Komugi
100) Jin-Roh
Source:http://aeug.blogspot.com/2006_08_01_aeug_archive.html#115497485355289130
I like SEED and all but I certainly don't think it deserves No 1. Not by a long shot. And since when was it and SEED Destiny considered the same show...
I'm glad One Piece got high up...but much of the rest of the results came out rather skewed. Pokemon beat Naruto? Guess the fillers really did hurt it.
But, regardless, this is why I don't put much stock in popularity polls.