There are so many, I know I'm going to forget some...
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Legend of Zelda: Majora's maskThe entire series is amazing, but this game stands out as clearly the best in my opinion. Other favorites of the series include Wind Waker and Twilight Princess.
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Fire EmblemALL OF THEM. Another great series. Can't wait for the 3DS one! (Cross your fingers for US localization :3)
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Yoshi's IslandOne of the best platformers ever.
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Luigi's MansionA very underappreciated game, I feel. Can't wait for the second one.
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Smash Bros.This goes without saying. Noticing a Nintendo trend, here? xD
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MetroidLots of great games in this series. I tend to prefer the 2D ones, and Fusion is my favorite.
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Age of MythologyAge of Empires games are great, but AoM was by far the best. I've always been interested in mythology, particularly that of Norse lore, so this was quite a treat. (Fun fact: my last name is derived from the god Odin. Etymology is FUN.)
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PokemonGen 1 and 2 are the only ones in my opinion. I almost hate to say it, but I think Silver is better than the originals. If so, only because you get to go back to Kanto
(Fire starters FTW!)
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CastlevaniaEspecially the GBA ones. Harmony of Dissonance <3
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MinecraftWhen I first started playing this game, before it hit alpha, I was addicted for a while. Haven't played it in some time, though...
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TerrariaAt first I saw this game as some sort of hybrid between Minecraft and Metroidvania. And it lived up to and went beyond expectations. It was actually the game that first brought me here
Ummm... I KNOW I missed a lot. I know it. I just love too many games xD