It's hard to top SNES with SMW,
ALTTP, Super Metroid, DKC1/2, Yoshi's Island, Super Mario Kart and Super Mario All-Stars. I'm a huge fan of 2D gaming.
N64 made up in quality what it lacked in quantity. Even though it represented the end of an era where Nintendo dominated the gaming industry, I think people remember the N64 very fondly. It had some of the very, very best games ever, including Ocarina of Time, Goldeneye, and Super Smash Brothers (not to mention the less refined but highly groundbreaking Super Mario 64).
The Gamecube era didn't produce as many "god-tier" games as N64, but there were a higher number of "great" releases. The Gamecube is often perceived as a failure, but it was not a bad system at all. Metroid Prime and Resident Evil 4 stood as the game's very best, followed by great games like
SSBM, WW, and Pikmin. Gamecube's biggest hole was an amazing Mario game. Sunshine was okay, but underwhelming.
The Wii was a commercial success for Nintendo and has been another solid system for the Nintendo gamer. Mario returned in a big way with the Galaxy games and NSMB. Zelda saw another solid entry with Skyward Sword and Retro delivered with a fantastic Donkey Kong game. Of course, the biggest story was more on the "casual" side of things with Wii Sports, Wii Fit, NSMB etc.