Just to be different: I liked the level in Catwoman where she was headed to the concert hall. You had to keep moving through the construction zone, as there was constant sniper fire on your ass...and the whole time shit's blowing up around you and the scaffolding is giving out under your feet. I still haven't managed to get a perfect score on that level.
The entire Metroid Prime. I've played that through at least 3 or 4 times. I don't know how they fucked it up, but the second one is missing something that makes it feel more like a bloody chore to play than any actual fun.
