The VGChartz list of the best co-op games for every system ever.

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Genesis games
Vapor Trail, basically a raiden clone, but a good one, plus one of the few co-op shooters on the genesis
Double Dragon, Very close to the arcade original but with a much much more stable frame rate.
Arcus Odyssey- 2 player action rpg
Forgotten Worlds- port of the arcade game, has a really strange glitch that causes the game to give you game over if you are using 6 button controllers, or have an emulator set as such

Snes,
Run-saber, basically a co-op strider
Pocky and Rocky 1 & 2, 2 player action rpg
Mr.Do!, arcade classic with an added co-op mode
Kirby's Dreamland 3