This is not a “best graphics on the NES” list. Just some games that I think are very good. I was going to point out some of the weaker artwork, but that seemed a little hypocritical, since I have a tough time making good looking pixel art myself. So, none of “they should have done this different”. Just good art pictures.
Starting with my favorites. I really like the graphics team over at Technos. The people who did River City Ransom, also made some similar looking games, like…

Super Dodge Ball

Crash N The Boys: Street Challenge
.
Here’s some other games in no particular order.

Kick Master

Joe & Mac

Ninja Gaiden III

Shadow of the Ninja

Batman – Return of the Joker

Chuka Taisen

Felix the Cat

Kirby’s Adventure

Fire ‘N Ice

Gimmick!

Ufouria (Hebereke)

Chip ‘N Dale Rescue Rangers 2

Stanley: The Search for Dr. Livingston


Little Samson (2 images)

Bucky O’Hare

Vice: Project Doom

Moon Crystal

Conquest of the Crystal Palace

Shatterhand

Gun Nac

Little Nemo: The Dream Master

Gargoyle’s Quest II

Megaman 2

Megaman 6

Castlevania III

Double Dragon III: The Sacred Scrolls

Gradius II

Radia Senki: Reimmeihen. This is probably the best looking RPG produced on the NES… well, Famicom anyway. Good work, Tecmo.
Sorry about the quality of some of these pictures. They are screencaps of videos. It would have taken me forever to play all these games to the right point to get better pictures.
I’m sure I left some games out. Lot’s of Disney games look very good. If you feel like a game is missing, and definitely should be in this list, feel free to leave a comment.