nesdev.org

I'm surprised no one mentioned the graphics from battletoads & Double Dragon The Ultimate Team.
that game has amazing graphics and coloring in various parts of the game. not to mention some of the best portraits for the end of level screens.
moon crystal looks fantastic too.

my all time favorite game graphically is the guardian legend for the fact that the backgrounds are not boring and the sprites are well done as well as least amount of flicker.
my two cents

TMNT 2+3 have some great graphics, how did I forget about that one I don't know...

Wizards & Warriors
Super Pitfall
Zelda II

All had unique art styles especially Wizards & Warriors. Super Pitfall is accused of being a Mario clone but it was actually staying true to the Tandy Coco3 and, for the most part, PC88 versions. Zelda II just seemed right. Less cartoony than its first outing.

One thing I wonder about later NES games is that they still didn't vary palettes between tiles in the large sprites they used. With stuff like MMC5 chips you think player sprites would be more colorful.