The perfect video game is the game that understands its technological limitations and options to an extreme degree, and then capitalizes in as many ways as possible; all without breaking the execution of the program.
The perfect game needs to run well, while also doing impressive things with its hardware. Anybody (kinda) can make a game that runs well; and anybody (kinda) can make a game that looks fantastic. For the perfect game, though, the developer must do both at the same time.
The perfect game also needs to have tight gameplay, meaning that there should be almost no input-lag/animation-lag/frame-lag/etc., and the player should be able to do whatever he/she is realistically-expecting to do, without unfair complications.
The perfect game will also have replay-ability; it will not be the game each time. It doesn't have to be total Minecraft-esque each time; but it should, at least, have some reason to play the game again. Even something as simple as side-quests, optional items, different endings, etc.
2D games age exceptionally well, because they are made with strict limitations in mind (most of the time).
There are too many to count.
If I absolutely had to pick one, though, I'd probably go with "A Link to the Past."
Second-place would be basically any early 2D Mario game.
(My favorite game of all time, though, is still Diablo 2 - which is a pseudo-2D/3D game.)
In terms of 3D, that's a bit tougher; but there are still plenty of options:
The very first thing that comes to mind is Majora's Mask. I think that one has enough replay-ability, while also being tight-enough, while also running well-enough (Though, that last bit is admittedly a stretch).
I'm also thinking about Ninja Gaiden Black, which is just a fantastic game (if you can find something to run it).
Halo: CE is also a fantastic choice, though it falls a bit short on the 'run well' part of the requirement.
Counterstrike is popular, to this day, for a reason.
I don't even like WoW, but damn is it ever-impressive.
I feel like Quake 3 and UT2k4 deserve a strong mention.
Max Payne 2 and 3, F.E.A.R., Project Gotham Racing 4, Resident Evil 4 (Wii), and maybe something like Skyrim or Witcher 3.
Perhaps Half-Life 1 and 2, or Far Cry 1, or a Tycoon game, or 3D Zelda.
There are tons to choose from.