Yeah, there are a few "rare" gamecube games.
Ikaruga, definately. There just weren't that many units created of the title, considering that, it sold amazingly well.
Skies of Arcadia Legends is another "rare" one
Cubivore is also quite rare. Yet again, simply because they didn't print too many copies because of the limited market.
I <3 all 3 of them.
Actually, Atlus itself, makes sure its games are "rare" products. They market them this way, they know they appeal to a niche userbase, so they seemingly don't make enough copies. Then, once theyre done with their small market penetration (one game per store, etc.) they can mark UP the price on their own games. Look at Atlus' website if you don't believe me.