For games as art, I gotta say the most likely candidate is I Wanna Be The Guy. It does exactly what art should do: it communicates from artist to consumer through a shared cultural language. In this particular case, it communicates shear, unadulterated, unbridalled rage and frustration, using the shared culture of experience with 90's era platformers.
I think Tetris is up there, too. Good art needs to transcend time. All too often, games are tied to their platforms, meaning modern audiences lack access or the ability to appreciate them. But Tetris has completely transcended platform. Every system has a version of Tetris, and everyone knows the game. It's simple in its rules, yet you can play it for hours and develop complex strategies along the way. From an art perspective, Tetris is the first video game to have achieved the same transcendent status as chess or checkers.
I'm very interested to see where Minecraft ends up. It's trending towards "art" for games for me. It provides people with a level of expression that is not available or accessible to most. The question in my mind is whether or not it will stay open-ended or become more linear and goal oriented. If it becomes goal-oriented, I think it loses a sense of "doing just for the sake of doing" that much art entails.
Most other games are just computer simulations of things that we'd do without computers. There's nothing special about the "Video" representation of the game, it's just a convenience factor. CRPGs make it so you don't have to do all the dice rolls on your own and provide a more produced story line than your DM could provide on his or her own. FPSs, racing games, flight sims, etc. are just simulations, not artistic representations. And when they add story telling, it's no different than movies. The video game aspect of the presentation isn't adding anything.
... With one exception.
"Call of Duty: Modern Warfare 2", the "No Russian" level. And not even for the "you kill the civilians" thing. It's the fact that you
don't have to kill the civilians, and most people didn't realize this. Everyone who had an opinion--favorable or otherwise--of that mission stuck to arguing the validity of killing "civilians" in a game. But the ultimate mind fuck came when it was revealed after the arguments settled that you could get through the level without shooting a single civilian. Nobody had tried! They just figured it was part of the win condition. Hell, I replayed that mission over and over again because I kept getting killed by the cops on the Insane difficulty, so failure to meet a win condition was not an unfamiliar thing. But not
once did I test the "kill civilians" assumed win condition. That says a lot about us as consumers of this technology, and it was only possible thanks to the unique experience of the Video Game as different from that of Movies.