Snowboard Kids 2 PAL is the rarest game I own, because it has only been released in Australia on the end of the N64's lifespan and Atlus games never being produced in high numbers. Some more N64 games I own seem to be rare given that you can sell them now for way more than their original msrp.
And probably some "day one" editions of games that aren't actually thàt rare.
I have a few games that I own that I know if I got graded, they are in good enough condition to be worth atleast $100 US Dollars. Those games are among my Gamecube library. I want to say maybe the rarest out of them all is OoT Master Quest. I also have the Collector's Edition game which I know only had a limited run as a promotional game to sell Gamecubes.
I don't think I have any single game that could be worth hundreds of dollars.
I own a few, The CDI games are just collecting dust, since I HATE them all, on the side of what I still play Rubiks games and Sim theme park for PC, however for windows 10 you need to patch them so they run with minimal crashes. I don't have any other rare games, but my brother has Super Buster Brothers for the SNES.
I own the LoZ Collector’s Edition for GC as well. I also have TP and WW for GC which as Jimmu said, aren’t necessarily “rare” but are hard to come by nowadays. Otherwise, I have no idea which of my games are considered rare or not..