Just recieved my new copy of Official Nintendo Magazine today (issue 80) and it include a feature on the top 100 games on Nintendo platforms.  They've limited themselves to one game per series, with only a few exceptions (such as Resident Evil and Zelda).  While they don't say it, I'm assuming that they aren't including games that have never seen a PAL release like they did last time, so don't expect the likes of the Mother/Earthbound games on this list.

100.  Super Monkey Ball (GC)

99. Little King's Story (Wii)

98. Tony Hawk's Pro Skater 2 (GC)

97. DJ Hero (Wii)

96. Trauma Centre (DS)

95. Prince of Persia: Sands of TIme (GC)

94. Conker's BFD (N64)

93. Killer Instinct (SNES)

92. GTA: CW (DS)

91: Pullblox (3DS eshop)

90. Beyond Good & Evil (GC)

89. DK '94 (GB)

88. Bit Trip Runner (WiiWare)

87. Tatsunoko vs Capcom (Wii)

86. WWF No Mercy (N64)

85. Fire Emblem (GC)

84. Sonic Rush (DS)

83. Prof Layton and the Curious Village (DS)

82. Mario vs DK: MLM (DS)

81. Duck Tales (NES)

80. Luigi's Mansion (GC)

79. Super Star Wars (SNES)

78. World of Goo (WiiWare)

77. Secret of Mana (SNES)

76. Silent Hill: SM (Wii)

75. Monster Hunter 3 (Wii)

74. Wario Wario Inc (GBA)

73. Sin and Punishment: SotS (Wii)

72. Goldeneye 007 (N64)

71. Mario Kart: DD (GC)

70. Super Castlevania IV (SNES)

69. Mega Man 2 (NES)

68. Zelda: OoA/S (GBC)

67. Donkey Kong Country (SNES)

66. Super Probotector (SNES)

65. Rock Band 3 (Wii)

64. Pilotwings 64 (N64)

63. Zelda: Spirit Tracks (DS)

62. Rayman Origins (Wii)

61. Resident Evil: Revelations (3DS)

60. Zelda: Minish Cap (GBA)

59. Super Mario Kart (SNES)

58. Golden Sun: DD (DS)

57. Kirby's Epic Yarn (Wii)

56. Super Mario Land 2 (GB)

55. SSB Melee (GC)

54. Zelda PH (DS)

53. Metroid Fusion (GBA)

52. FFIII -unfortunately the 'real' III, seriously wtf? (DS)

51. Perfect Dark (N64)

50. Eternal Darkness (GC)

49. DKCR (Wii)

48. Super Mario Sunshine (GC)

47. Soul Calibur II (GC)

46. Paper Mario: TTYD (GC)

45. Advance Wars: DS (DS)

44. Starwing (SNES)

43. REmake (GC)

42. Mario & Luigi: BIS (DS)

41. F-Zero X (N64)

40. Banjo-Kazooie (N64)

39. Metroid Prime 3 (Wii)

38. Super Mario RPG (SNES)

37. DQIX (DS)

36. Wii Sports Resort (Wii)

35. Mario Kart 64 (N64)

34. Super Mario Bros 2 (NES)

33. NSMBWii (Wii)

32. Chrono Trigger (SNES)

31. Okami (Wii)

30. Prof Layton and TLF (DS)

29. Xenoblade Chronicles (Wii)

28. Pikmin 2 (Wii)

27. Zelda: Link's Awakening (GB)

26. Super Mair 3D Land (3DS)

25. Zelda: MM (N64)

24. Star Fox 64 3D (3DS)

23. Pokemon HG/SS (DS)

22. Mario Kart 7 (3DS)

21. Zelda: TP (Wii/GC)

20. Super Metroid (SNES)

19. Animal Crossing (GC)

18. SMW2: Yoshi's Island (SNES)

17. Metroid Prime (GC)

16. Tetris (GB)

15. SSFII (SNES)

14. Super Mario Galaxy (Wii)

13. Zelda: ALttP (SNES)

12. Resident Evil 4 (Wii)

11. Super Mario Bros 3 (NES)

10. SSB Brawl (Wii)

9. Zelda: WW (GC)

8. Super Mario World (SNES)

7. Super Mario 64 (N64)

6. Mario Kart Wii (Wii)

5. Pokemon Black/White (Ds)

4. Zelda: OoT 3D (3DS)

3. Super Mario Bros (NES)

2. Zelda: SS (Wii)

1. Super Mair Galaxy 2 (Wii)

My thoughts:

FFIII instead of VI, or even IV DS - Bullshit, really can't understand the logic here.

No Terranigma - Regrettable, but understandable given it's not the most well known SNES game

Mario Kart Wii > 7 - Suprised by this

Galaxy 2 @1 - Don't really disagree with this too much, it's my favourite game of the 7th gen

Fire Emblem only 85? Sadness...

Well my list would look completely different but meh, who cares...

Xenoblade over Chrono Trigger? WTF

Where is Uncharted 2! This list is obviously biased towards games on Nintendo platforms.

Ocarina of Time not in the top 3.

I like this list.

I agree with Carl.

Also, FF3 was abysmal, I wonder how it got so high.

Little disappointed they seem to have forgotten Wave Race (either of them)

Rayman Origins!

A poor list in my opinion. Has very good games on it, but it looks like it was rushed.