I think most critically acclaimed games of the era have aged well, much better than a lot of early 7th gen games.
The good thing about 3D games from the 5th generation was that there were no established rules for how to make a 3D game, so there was a lot more variety in how they played.
But to name a handful:
Doom 1
Doom 2
Half-Life
Mega Man 2
Super Mario Bros 3
Super Mario 64
The Legend of Zelda: Ocarina of Time
Streets of Rage 2
Sonic the Hedgehog 2
Nights into Dreams
Panzer Dragoon zwei
Panzer Dragoon Saga
Sega Rally Championships
Virtual Fighter 2
Crazy Taxi
Tempest 2000
Galaga
Castlevania (most games in the series)
Contra series
Spyro series
Soul Calibur