There is a surprising lack of cooperative games from this time in gaming history, as a perusal of the Co-Optimus database shows. The mid to late 90s had a push for 3D in games, and due to console system limitations, adding in more players for this type of game was very difficult. The side-scrolling brawlers and shmups, very important to co-op in the early 90s, had fallen out of favor. It would be several years before the explosion of cooperative games for the next generation of consoles, the Xbox, Gamecube, and Playstation 2. Nontheless, there were still a handful of co-op highlights on the Nintendo 64 that deserve mention.
The Gauntlet series is one of the oldest and most hallowed in co-op gaming history. Gauntlet Legends brought the series into 3D, first hitting the arcades and then home consoles shortly thereafter. The classic gameplay, with Wizard, Warrior, Valkyrie, and Elf, held up quite well on the N64, adding in a level up system and excellent (though now dated) graphics to the winning formula. Gauntlet Legends supported four players, and was one of the few co-op games to do so, though the Expansion Pak was required.
Fan-favorite developer Rare published this quirky, unique game in 1999. A third person shooter, Jet Force Gemini featured platforming elements, with plenty of levels to explore and power ups and other items to collect. Co-op was included, but it wasn't exactly stellar. Player two could control a robot that followed the main character through the levels, and could assist in shooting the bad guys. Sounds like an early version of BYOB co-op, but hey, any co-op is better than no co-op, right?
Another smash hit by Rare, this shooter was a follow-up to the mega-popular Goldeneye 007. A futuristic setting, a tough-as-nails female protagonist, and split-screen two player co-op set Perfect Dark apart from the FPS pack. The game was likely the best-looking Nintendo 64 game ever, and was a critical and sales success. M-rated Perfect Dark showed that the squeaky clean, family image of Nintendo could be tweaked to great effect.