Ehhhh
I really like a lot of games, and a lot of them are hard to compare objectively due to how different they are.
I'm going to say Sonic 3 and Knuckles. (This choice is largely based on opinion and nostalgia, so take it how you want to)
I still remember when I figured out that you can hook another cartridge on top of S&K.
All my friends only played the new Sonic games, so none of them believed me when I told them about the existence of Hyper Sonic.
When I showed it to them I became a legend among my friends.
It's a rather tough question and there's still a lot of game design qualities which we don't have 100% objective measurements for.
It'll either be Nintendo or Valve's camp, though, because as much as I hate to admit it, they do spend a lot of time with geniuses who understand how the human works trying to make games that teach.
I don't think we're at the stage where we can pick one specific game out, though.
I really agree with this. At this point, the quality of a game is mostly subjective.
Nintendo and Valve games do get waaay up there though, and I don't think many people can reasonably disagree with that.