LogFAQs > #908877265

I voted Silent Hill 2 out of those. I also have some respect for Xenogears (a game I want to play again,) and Telltale's Walking Dead.

My actual favorite is Mother 3, though. It makes such good use of the medium, using things like in-battle text and variations on RPG examine text to help tell the story. Even though the main characters hardly ever speak it characterizes them pretty well using sequences that deal with their inner minds - it still manages to tell a very personal story. The soundtrack is also organized to draw connections between different areas and sequences, which do a lot to enhance the emotional impact of the story. The final battle is still the most emotionally draining thing I've seen in a game.

Honorable mention to Shadow of the Colossus. Excellent minimalistic storytelling in that game. The twist is great in that it isn't actually a twist but still surprises a lot of people, which does a lot to enhance SotC's particular themes. I voted for SH2 for similar reasons. It's understated and heavy on symbolism.