I have so many favorite games by Nintendo,but my number favorite one now is pretty much the Mario Kart series,so fun! right now picking one, I'll go with Mario Kart Wii!
It's hard to pick just one. These are my top choices, depending on system;
Super Mario World for the SNES for its classic, yet enjoyable simplicity. It was one of my first games I've played that I can remember, and is still a good game to play once in a while.
(There's also Megaman X1, X2 and X3 for that genre.)
For the N64, I gotta say Ocarina of Time. There are so many things about it that I enjoy; the story, the different settings, etc. I don't think I've re-played any other Nintendo game that many times (the gold label has worn off of the cartridge).