I second that.internutt said:The final area of Majora's Mask inside the moon.
There was something really sinister about the green field with a single tree in it. The rest of the game was full of really weird and wonderful areas and this one really stood out as creepy, if only for feeling out of place.
Also, the final area in Metroid Prime. The freaky music and those annoying as hell Fusion Metroids, not to mention the red Phazon. It feels different from the rest of the game and can easily be set apart from it. I also think it's the best ending out of all three Prime games.
And I'm sure I'll get punched in my internet face for this, but part of the final level of Halo 3 made me smile. They did a good job of transfering the original Halo's control room to 3's graphics, and it was very exciting. Sent shivers up my spine... to bad the rest of the level kinda sucked.