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I'd say the N64 was pretty influential when you consider Mario 64 pretty much wrote the book on 3d movement and camera control on consoles, Zelda invented the lock-on camera, and the console popularized multiplayer in a way which wasn't possible on other systems before or at the time but which became the standard afterwards.

Popularity is one thing, but a ton of the core of modern 3d game design is based on mechanics which originated in N64 games. I don't think it's as influential as the NES or Atari 2600, but in my opinion it is the most influential console for 3D gaming.