This is going to be a difficult list to do because there are lots of amazing games in Nintendo's history, but im sure this NeoGAF list will be more competent than the shitty Famistsu one.
1. Super Mario Galaxy 2 Best 3D platforming EVER. One of the most amazing games ever created. And the music... OMG.
2. Super Mario World Best 2D Mario, tight platforming, best objects in the series (yoshy and feather), best world map, best 2d music (dat castle theme)...
3. Metroid Zero Mission Its very tied with Super Metroid, but Zero Mission is so nice had such a blast playing it many times. Best remake ever done. And the final part is exciting. And I love the credits music.
4. Super Metroid Nearly tied with Zero Mission the game is amazing. An epic scale Zebes with awesome bosses and platforming. And has my favourite track of the series, Theme of Samus. "See you Next Mission!" *salutes*
5. Super Mario Galaxy While some stages are better in its perfect sequel, this one gets lots of points for some of its magnificent tracks and the story. Yeah the story. It was perfect, epic, and at the same time I didnt think it stopped the pace of the game. And the storybook is one of the most beautifull things Nintendo has ever done.
6. Super Smash Bros Brawl I could have put perfectly Melee here because ive played more hours to that game with a friend than any other. But Brawl is here because it the best museum of Nintendo history ever done. The music, the stages, the characters, the trophies, the stickers... The only thing I dont like is the story, I could have wrtitten a better one using all of nintendo's history instead of the shitty thing the writer of FFVII wrote. Although the intros were awesome.
7. The Legend of Zelda Twilight Princess So hated only some years ago I always have loved Twilight princess. Its true I didnt beat Ocarina when it was released, or the same as Majoras Mask. And even if also my favourite Zeldas are Links Awekening and Link to the past, I REALLY love TP. The scale, the dungeons, the bosses, the story and Midna (best sidekick in any Zelda), thats what makes TP great. yeah it could have some changes here and there for the better (things I would mix with Skyward Sword), but i had a blast the first time I finished the game.
8. Star Fox 64 3D Or Star Fox 63 in the original, ive placed the 3DS one because it looks so much better, and it has more score attack modes. Ibe beated this game so many times I cant even count them. Its so much fun. Also props for the awesome castillian spanish dub NoE made for 3DS. The original is amazing, but the spanish one has the same charm (well, Falco could have been better). Alfonso Valles <3
9. Punch-Out!! Wii One of my favourtie games ever was the original, this ones blasts it out of the water. The animationof this game is the best cartoon animation any studio has made for any videogame. Is just that good. The gameplay is PERFECT. The music is amazing, the characters are even better than in the original (the voices of each one in their own language are goldly) and the just oozes humour. Next level Games <3
10. F-Zero Climax (Imported) My favourite F-Zero. Best F-Zero mode 7 there is. Challenging (but not frustrating like GX), you can make your own tracks, biggest roster of characters, and best music in the series (the remixes are out of this world). GX could have been here if it were not for the shitty music or the over rubberbanding difficulty. Too bad a very little number of people have played this game.
Honorable mentions: F-Zero GX, Ouendan, Elite Beat Agents, Punch-Out!! NES, The Legend of Zelda: A Link to the Past, The Legend of Zelda: Link's Awakening, Metroid Prime, Super Mario 3D Land, Metroid Prime 3: Corruption, Super Smash Bros Melee, Conker's Bad Fur Day, Mario and Luigi SuperStar Saga, Metroid Fusion, Metroid Other M, Star Fox, Golden Sun, F-Zero, Kirby SuperStar, Mario Kart 7, Ocarina of Time, Super Mario 64...
And the list could go on an on. Fuck you Nintendo for creating so much amazing games.
And the 10 list was very difficult to do, is not that they are really separate in numbers because of which one I liked best or quality, as they would come all very near in how awesome they are, even some honorable mentions.