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Of all time? Probably one of the early Dragon Quest or Final fantasy games given they had an impact on multiple generations. Or Monster Hunter 3 since that series jumping to Nintendo - for a time, exclusively - was big.  This is a much more interesting question on a per generation basis though because the answers become so wildly different.

For example, I would say Dragon Quest or Final Fantasy would take the cake for the NES and then Final Fantasy VI for the SNES, but then on the N64 I instinctively go for Doom 64. Having the official sequel to Doom and Doom 2 as an N64 3rd party exclusive really cemented the system as a heavy hitter in the emerging shooter genre. And then Resident Evil 4 on the GameCube is probably the biggest given the cultural impact since no game really transformed the sales trajectory. Wii is Monster Hunter 3, that series jumping to Nintendo was huge. Wii U is probably an indie game, maybe Fast Racing Neo as that really gave a lot of momentum to Shin'en, or Shovel Knight because it is kind of emblematic of Nintendo's embracing of indies as a big part of their library. Switch I think it's Doom 2016, no contest. That was the game that came out and everyone sat up and paid attention and was the beginning of Nintendo recovering the third party support lost over the course of the late Wii and Wii U eras.