AyreonMaiden said:
Legend of Zelda: Majora's Mask. It perfectly deconstructed the comparatively childlike innocence of Ocarina of Time.
It's a quirky, dark, and completely emotional story about the impossibility of the storybook heroism, the power of forgiveness, the value of your "home," the virtue of selflessness, and the weighing and acceptance of responsibilities in quite possibly the most realistic pre-apocalypse scenario I've yet seen in a game.
And those are just the themes I could think of off the top of my head. There's so much more in there. I really wonder how accidental all that subtext really was when Eiji Aonuma led his team in the making of it.
I'll agree that Majora's Mask is really a pretty good "games as art" argument. It's got a ton of layers to the world and the story that make it amazing, but also incredibly offsetting.
But I'll also say that the Metal Gear Solid series (especially 3 and 4,) are amazing in terms of the emotion, even if the plot does get random at times. And while I'm sure that people'll say "well the plot in those games might as well be a movie!", I think that that emotion does depend quite heavily on the gameplay, to immerse the player in the character. Again, especially 3 and 4.