At the top of my head at the moment, though I'm not sure if some of these are available for purchase...
-EDIT-
NES: Sweet Home (has a fan translation)
SNES: Zombies Ate My Neighbors, Star Ocean (has a fan translation), Chrono Trigger, The Ninja Warriors, Battle Clash and Metal Storm, Terranigma
Genesis: Rocket Knight Adventures, Contra: Hard Corps, Mega Man: The Wily Wars, M.U.S.H.A.
PS1: Threads of Fate, Tales of Phantasia, Ghost in the Shell, Parasite Eve, Vagrant Story, Valkyrie Profile, Elemental Gearbolt, Grandia, Klonoa
Wii: Kirby Dream Collection, Fragile Dreams: Farewell Ruins of the Moon (thankfully it isn't redunk expensive unlike Xenoblade or MP: Trilogy), The Last Story, Klonoa (remake)
GBA: Klonoa 2
I would say Doom 64, but I'm not sure if you're interested in old FPS games. And no, Doom 64 is not another port of the first Doom game, Doom 64 is an entirely different game.