Retro is a pretty massive category at this point. That's what, like 40 years worth of gaming? Somewhat hard to pick just one.
For me, at the moment anyway, I'll say Ocarina of Time. While it's by no means my favorite Zelda game, it is one of the best paced ones, especially among the 3D games. It's also one of the single most foundational games in the 3D action-adventure genre, with tons of modern games still using its basic bones.
I'm sure my answer for "best retro game" will change within the day.