Super mario rpg legend of the seven stars
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I'm not sure if I have any rare games, but I guess Arc The Lad Collection and the first Shadow Hearts game could be considered rare.

Pokemon Box (GCN)
Cubivore (GCN)
Ikaruga (GCN)
Chiller (NES)

Yes you may consider the Arc the lad collection rare, scary...

Here goes. don't know exactly if all are rare though.

Shadow hearts (series)
Final Fantasy 7 (original and platinum)
Final Fantasy 8 (original and platinum)
Final Fantasy 9 (original and platinum)
Final Fantasy Anthology, with music disc
Final Fantasy 6
Parasite Eve, with Squaresoft collectors disc
Vagrant story, with collectors disc
Legend of Legaia
Brave Fencer Mushasi
Chrono Cross (original)
Xenogears
Vandal Hearts 1 and 2
Saiyuki journey west
Lunar silver star story
Saga frontier 2
Grandia
Alundra
Breath of fire 3 and 4
Metal gear solid
Granstream saga
Suikoden 3

And i think those are the rarest...

- SF Alpha 2 (SNES)
- Rival Schools (PS1)
- Marvel vs Capcom 2 (PS2)
- Capcom vs SNK (PS2)

...i just noticed they're all Capcom games lol

Wii Fit.

Just bought Ogrebattle64 for 42$ on ebay. Now this is the rarest game I own.

Jump Ultimate Stars(DS)
Elite Beat Agents(DS)
Skies of Arcadia Legends(GC)
One Piece Unlimited Adventure(Wii)

The only rare game I own is Marvel Vs. Capcom 2 (for PS2 if that counts)

I forgot all about MVP Baseball 2005 for PC.