Here are some that I would recommend. Got me nostalgic with the SNES list. I've not played any SNES or N64 game in so fucking long!
N64: Zelda: Ocarina of Time, Super Mario 64, Killer Instincts 2, Goldeneye 007, Super Mario Kart 64, Waverace, Turok, Duke Nukem: Zero Hour, 1080 Snowboarding, and WCW vs. NWO: Revenge
Turok was really fucking hard. I never beat it as a kid without cheats. Also, Duke Nukem: Zero Hour was really fun, but damn, another one I never beat as a kid. I remember those two games were fucking hard as fuck.
PS1: Metal Gear Solid, Resident Evil: 1/2, Saga Frontier (but you might want to try the remake instead)/2, Legend of the Dragoon, Chrono Cross, Syphon Filter, Super Puzzle Fighter (might want to try the HD remake, though), Street Fighter EX: Plus Alpha, Need for Speed: Hot Pursuit, Thrasher: Skate and Destroy, and Symphony of the Night
SNES: Super Mario RPG, Teenage Mutant Ninja Turtles: Turtles in Time, and Donkey Kong Country 2, Battletoads and Double Dragon, the Lawnmower Man, Sunset Riders, Killer Instincts, TMNT: Tournament Fighters, Donkey Kong Country 1, Super Mario Kart, Super Castlevania: IV, Street Fighter: II Turbo, Super Mario World, and Super Mario: All Stars.
Some don't hold up too well anymore like all the FPS games. Just a system that really deteriorates without a great storyline. The RPG games and racing/sports games all hold up really well. Fighting games don't really hold up well unless they are discontinued: KI series and TMNT. DKC still holds up well, but the soundtracks for both games are some of the best ever. I would recommend playing them only because of that beautiful soundtrack.