It's too hard to narrow this down to one. In no order:
Secret of Mana. I played it multiplayer with my brother during the summer holidays. The most magical, perfect game. It captures everything great about child-like adventure and if there's a better video game soundtrack, I've yet to hear it. Honourable mention to FF6.
Ico. Sombre, touching. It showed how gown-up video game stories could be and how they should be told - through gameplay, not cutscenes.
Rez. Rez blew my mind. On the Dreamcast, on the PS2, the remake on 360, and now, today, on PSVR. Unique, timeless.
Street Fighter 2. Nothing else needs to be said.
Mario 64. During the NES and SNES days Mario was the 2D platform game. And then suddenly it was in 3D, completely different yet exactly the same. A genius Mario playground. The fact that Nintendo managed this again with Ocarina of Time shows how on form they were at this point. No other developer has managed a similar feat, and they did it twice.
Golden Eye. See Street Fighter 2.
The Last of US. The Last of Us is similar to Ico in many ways. They both tell a story through gameplay and how the lead characters interact with each other. It's the most touching, well told, grown-up story I've experienced in a video game.