I have a handful of SNES games that would probably be considered rare - Chrono Trigger, Super Mario RPG, Secret of Mana, and Mega Man X2 (the latter three games I actually snagged at the local retro game shop for pretty low prices about a week ago, Secret of Mana just YESTERDAY! ) Probably over half of my Super Famicom collection is rare, but since I see these games all the time in Japanese auctions selling for ridiculously cheap, I don't really know if they're rare or not... Cases in point: Star Ocean and Bahamut Lagoon, maybe a few more.
Okay; all are complete (unless noted), US version, and in excellent condition (all):
Saturn: Panzer Dragoon Saga, Guardian Heroes, and Shining Force III
Dreamcast: Marvel Vs. Capcom 2
Sega CD: Lunar Silver Star & Lunar 2 Eternal Blue
SNES: Chrono Trigger (map and cartridge only), Secret of Mana (complete), Mega Man X2 & 3 (games only)
Gamecube: Zelda Collector's Disc, Ocarina of Time/Master Quest, Metal Gear Solid Twin Snakes
PS1 (here we go): Lunar Silver Star Story Complete (EVERYTHING), Lunar 2 Eternal Blue Complete (EVERYTHING), Grandia, Final Fantasy VII-IX (black label), Tactics Ogre, Persona 2 Eternal Punishment, Star Ocean The Second Story, X-Men vs. Street Fighter.
PS2: Every MegaTen game (Devil Summoner 2 is still sealed w/Plushie), Growlanser Generations (Game itself is SEALED, no outer carboard box but EVERYTHING is there and I got it for 55 bucks).
Systems Owned: NES (1), NES (Top Loader), SNES, N64 x 2, GC, Wii; Master System I, Genesis Model 2, Sega CD Model 2, Sega 32X, Sega Saturn, Sega Dreamcast (US), Sega Dreamcast (JP); PS1, PS2, PS3; XBox; Neo Geo, Neo Geo CDZ; Game Boy (orig. Gray), GBA, GBA SP, DSi, 3DS; PSP (1000), PSP Go; NGPC.
The rarest game I currently own is probably a Rendering Ranger cart for the Super Famicom. What is great about this game though is not the extortionate price it oftens goes for but the fact that it is a pretty decent shooter that shows off what the Snes can do.
I own all of the rare Saturn US releases, and many of the Japanese ones such as Radiant Silvergun and the Shining Force 3 Premium Disc. I also own the rare N64 games (Ogre Battle 64, Harvest Moon 64, etc.), along with some rare NGPC games such as Faselei.
However, one of my lesser known gems is actually a PC game; Quest For Glory Anthology in the original large box. I'm pretty proud of this one.
I've got a Megaman V cart for Gameboy with a very near mint label. Picked it up for about 10 bucks a few years back, and I've seen really nasty looking ones get sold for like 30 bucks, I'm guessing if I wanted I could easily get 60 for mine.
I also have a very rare Japanese bootleg of pokemon green. Most pokemon bootlegs are well documented online, but this one isn't. Probably because its one of the highest quality bootlegs I've seen.