We have NES games still lying around, so those probably count (though I haven't played them outside of Xenophobe briefly as a kid):
1943: The Battle of Midway
For Nintendo 64, I'd have to say Extreme-G and Asteroids Hyper 64, though I'll go ahead and say Quest 64 as well. I doubt any of those count as rare, honestly, but they're at least obscure enough, I suppose. Maybe.
We have a lot of GameBoy Color games that I can't really list them all that might be rare. The Simpsons Tree House of Horror game might count, now that I think about it... there's also the Scooby Doo Classic Creep Capers GameBoy Color game. Not sure how well that sold despite the GBC game having a better score than the N64 version.