Brothers: A Tale of Two Sons - which is the best game you've never played.
Always here people going on about that one, but checked it out and it just didn't appeal...
For me I would say the original
GTA. 3 may have made the step to 3D, but none of that, or any of the games that that spawned would have happened without the brilliance of the original. It may only be 2D, but it was pretty much perfect at what it did, and in many ways tbh I sometimes would rather play it that way than in 3D.
Quake. Kind of the opposite reasoning here. Wolfenstein, Doom, Duke 3D were all great games, but Quake was the first FPS to have real 3D, great graphics for the time, the type that age well as the artistic quality was so good, one of the first quality MP games, and possibly the first professionally competitive MP scene, and 1st gaming 'star' (a guy called Thresh I think), basically launched the modding scene, and had many games or staples of FPS games that grew out of it's mods (and CTF style games, Team Fortress to name two), a decent single player game, and the best model for a Freemium game going ('Demo' was the whole 1st episode, then you had to buy ep2-4). Launched the careers of iD and Romero (Deus Ex) into the stratosphere.
After that I don't know. A Mario or FF game would be a good shout. For me personally probably something like
CM3. The first one that I lost days and days to, and I think that was when it really started to turn into the game it is now, with increased depth and detail, but not the possible overkill they have nowadays. Oh and it wasn't a whole new game every year back then either iirc!