One from each console that I own:
NES
Teenage Mutant Ninja Turtles III: The Manhattan Project
Overlooked because it came out a few months after the SNES had been released and while Turtles 4 was in arcades and soon to come to SNES.
Nintendo 64
Jet Force Gemini
Not sure how overlooked this is since it is a Rare game, but had a quasi metroidvania feel to it if you were collecting everything.
Gamecube
Metal Gear Solid: The Twin Snakes
Gamecube remaster of the Playstation classic. Graphics are greatly updated as well as adding in abilities that were added for MGS 2.
Wii
Zack & Wiki: Quest for Barbaros' Treasure
First non-Nintendo game that used the Wii-mote with a real purpose instead of just waggling, as well as a tough as nails puzzle/point and click game.