I'm not sure how rare any of my games are, but my girlfriend has a nice and hard to find game. She has Shantae for the GBC, and last I checked, it was going for around $230. It's one of her favorite games ever, so she's not giving it up anytime soon (or ever).
As for me, here's what I think may be "uncommon" in my collection, as I'm sure none of it is rare:
Mega Man X1-3
Mega Man I, II, and V
Eternal Darkness: Sanity's Requiem
Wario's Woods (SNES, not the NES version)
Phantasy Star Online 1 and 2 Plus (I bought PSO1&2, only to find out the disk was for 1&2+. Silly Gamestop)
Game and Watch Collection (It's only rare because it's a Club Nintendo game)
Metroid II (Just bought yesterday)
All good games, but nothing too out of this world.