These two:
The Interloper cutscene from Legend of Zelda: Twilight Princess. At first I thought it was just weird and creepy, but later I realized that for those that pay attention, this scene contains a lot of symbolism. It's very well made artistically and the scene is basically the definition of the tone of the game. Twilight Princess actually contains many great cutscenes. I'd give the honourable mention to the Ganondorf's execution scene at the Arbiter's Grounds.
And 'Revan's Revelation' from Knights of the Old Republic. This video includes the lead-up and the aftermath, but I think those should be included to understand the full context. Darth Malak's monologue is quite essential. When I first saw this scene, it completely blew my mind. How did I not see? All the clues were right there, as flash-backed by the cutscene. I am Revan, and I never knew! Utter brilliant game story wrinting, and one of the best games ever made overall. There's just two things EA could possibly do to make me buy a game of their's again, one of them is letting Bioware make a KotOR 3 that's as perfect as this one.
