The rarest game I own would haved to be Earthbound. Unfortunately I don't have the box and all. Yet I believe the cartridge by itself brings around $80-100, simply for being desireable. I've seen complete sets with box and strategy guide selling for around $400 or so.
I have a couple games that aren't really rare as much as desireable for SNES, Final Fantasy 2, 3, plus Secret of Mana. I've got the box and map and booklet for Secret of Mana, and I believe it tops around $60 or so. Yet, it's on Virtual Console now so the value now might have gone down.
I found this site for rare NES games. http://www.racketboy.com/retro/nintendo/nes/the-rarest-and-most-valuable-nes-games
Out of my collecion I only have 2 of these games, Dragon Warrior II and Teenage Mutant Ninja Turtles Tournament Fighters. I'm surprised that other games I have like Yo Noid!, Tiny Toon Cartoon Workshop, Faxanadu, Final Fantasy, gold Zelda or black Shinobi cartridges didn't make the list. Makes me wonder how rare My Virtual Boy is.