Metroid prime 2 Echo's has a sort of multiplayer.
splitscreen vs. (screen split in 4)
You could find echo's as a gamecube title, or rarely as a japanese Wii game (upgraded with wiimote controlls)
But the rarest is the Metroid Prime Trilogy (which I have, EU version though). Seems like they only made a couple of hunderds or thousands of these :s
Lemme see.
Kirby on the GBA had coop (the one with the mirror at least had)
"new" title.
Super Motherload (that old browser game has been remade and is on steam now)
4 player coop
Those are the ones that came to my mind (which aren't on the list yet)