Many, but if I have to choose only one, Chrono Trigger. Everything is perfect on this game, music, characters, story, enemies, graphics. It's my favorite game of all time.
And they're still making incredible hacks of it to this day! The modding scene for OoT has come a long way, especially in the last 10 years.. Crazy that people will mod a game that's this old, for this long.. Lol.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.
Serious:Castlevania I, Zelda II, or Ninja Gaiden on NES.