Mystical Ninja Starring Goemon - It's personal to me, its not objectively the best game ever as it definitely has its flaws, but its my absolute favorite and it takes from 2 of my favorite games and adds a wacky edo-era Japanese spin to it. Also has an amazing soundtrack.
Super Mario 64 - Was my first N64 game and its still holds up as the best 3D platformer even to this day. Nothing tops this one yet.
Legend of Zelda Ocarina of Time - I don't think anything has to be said that hasn't been said before.
Legend of Zelda Majora's Mask - ^