World Driver Championship, especially the Zurich, Las Vegas or Sydney tracks, incredible visuals for the time, the best looking "realistic" racer of that generation by far. Too bad BOSS games folded, they had an
awesome looking Xbox game on the way as well
Perfect Dark did things that STILL aren't done by many games today in the hit detection, animation, lighting and AI department. Not to mention attention to detail like many types of bullet holes depending on the surface, enemies
staying limp when shot on foot (and not miraculously recover like all other games) etc . All that on 8MB RAM on the N64. Amazing. Any other console shooter at the time couldn't hope to come close.
Banjo Kazooie Had great colors, incredible draw distance (see the Click Clock Wood level or the Haunted Mansion), smooth framerate 99% of the time.
Roadsters was an unexpected surprise sepecially with the xpansion pak's hi-rez mode it really looked very clean, shiny and busy, lots of trackside detail, with fully rendered drivers on the cabrios. Could pass as an early DC game, even.
Diddy Kong Racing Best looking and best playing kart racing game of that generation. Flawless visuals basically.
Battle for Naboo Perfecting the Rogue Squadron engine, ditches the fog entirely, super hectic levels, had great audio AND a commentary feauture by Factor 5 on the cart.
Indiana Jones Improved from the PC version, with better textures and lighting. Great visuals and framerate. The closest thing to N64's Tomb Raider
Legend of Zelda Majora's Mask
No need to say much for this, they trumped OoT visually, in enemy numbers, animation, effects, and the polycount was the highest of an N64 game (along wth JFG)
Honorable mentions
F1 World Grand Prix II Was the best looking F1 sim at the time, with "photorealistic" visuals.
007 TWINE Much better lighting, reflections, shadows,reload animations geometry than GoldenEye. However had worse textures imho.
Jet Force Gemini Gargantuan levels, really large scope, great lighting, some fuzzy textures in places and framerate drops nix points.
Conker Same as above, only more pronounced
Rally Racing 2000 It was an OK rally game with good draw distance but it was the first time i had seen a
true real time reflection of the environment on car windows and windshield
ISS 64/98/2000 Arcade football game (precurson to the PES series) that looked incredible at the time. The 200 version even supported 480i visuals with the expansion pak.
GoldenEye
Though it got beat by Perfect Dark's evolution it still impresses at times (Aztec, Silo and Frigate levels have amazing texturework)
Pilotwings 64
Launch game, incredible scale, large draw distance.