This one's quite close to call for me. Several great games that I've played and enjoyed over the years, but nothing that's quite among my all-time favourites. There's Super Mario RPG, Crash Bandicoot (the image in the OP is from Crash 3), Super Mario 64, Tomb Raider, Resident Evil, Mario Kart 64, Red Alert, Duke Nukem 3D, and more. All great games, especially for the time, but I'd say in almost all of those cases, later games in their respective series have vastly improved on them.
For me, this ultimately came down to a choice between Super Mario 64 and Red Alert. I'd say in terms of quality they're roughly equal, though obviously very different in genre and style, so I'll pick Mario simply because of its greater influence overall. Red Alert was more of an improved iteration on mechanics introduced in previous games by Westwood, but Mario 64 effectively established the foundation for 3D platformers going forward.