Sorry, but it's hard to pick just one.
C&C: Red Alert really had several epic levels, and for various different reasons. I loved the way the game mixed up the missions.
Also, it might not seem as impressive anymore, but the first couple levels of the Reactor unit in Quake II (where you drop down and fight a tank commander at the very beginning, and then the next one with the power stacks that you flood later) kinda blew my mind at the time when I saw it. Hell, the id games have always been the golden standard for level design imho (up until Doom 3... and I never played Q4).
Beyond Good and Evil had some really outstanding levels too. The part where you have to run away across the rooftops.... fantastic! One of the better moments I've seen done in a game.
The Thief series also contains several examples of the very best level design out there.
Finally, I'd like to mention the original Phobos Moon Station from Unreal Tournament as one of the greatest (and my personal favorite) deathmatch arena level ever made.