Uncharted 1 and Super Mario Sunshine.
...
...Okay, seriously. It'd be hard for me to narrow it down to a select few, so I'll just roll off a bunch.
1. Paper Mario - Glad somebody else already mentioned this one. Such a great fight. I didn't think Nintendo would still be capable of creating a Bowser battle with a great atmosphere anymore at that point, and I was wrong.
2. Metal Gear Solid 4
3. Final Fantasy VIII - The whole thing, just great atmosphere, great music, etc.
4. Ratchet & Clank: Up Your Arsenal
5. Donkey Kong Country 2
6. Sonic 3 & Knuckles
7. Bowser's Inside Story
Maybe more, but that's good for now.
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