That's a really good question. The original Kirby's Adventure comes to mind. It struggled a bit on the NES hardware, so there's some slowdown and input delay. Really fun game, though. I hear the 3DS version corrects that, which intrigues me.
EDIT: You know, the original Silent Hill may qualify. It's a well-made game, but I think there's a bit of input delay. It's been a while since I've done a playthrough, but it is still among my personal favorites.