I always felt Battletoads looked amazing on the NES and it had such good variety in levels, but I believe on a technical level, 3D World Runner will probably take the cake.

battle toads and mario 3.

I agree with Batman Return of the Joker.

First game that popped into my mind was Super Mario Bros 3 so i'm going to go with that

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They always had a thing for 3d worlds 

Punch-Out for me, those huge sprites blew me away as a kid... Battletoads & Kirby both look superb!

Battletoads is definitely among the best. Like Return of the Joker, it could almost pass for a low end Megadrive/Turbografx-16 title

Well, the game actually was released on the Mega Drive:

Ninja Gaiden 3 has some ridiculously awesome graphics for an NES game.