Red Zone for Genesis. Great 3D effects, full screen rotation done in software, full motion video clips, and one pumping soundtrack. The gameplay is actually pretty sophisticated too. Shame it's way too hard.
Gran Turismo 4 deserves mention for getting 1080i out of a system that totally doesn't support it. I still don't know how that works.
Dragon's Lair for the Game Boy Color is pretty amazing.
Anyone remember Hydra for the Lynx? I thought that game compared favorably to games on Genesis and SNES. Actually it's pretty on-par with GBA.