[quote name='Epiphonestrat']Beyond Good & Evil, Prince Of Persia: The Sands Of Time and The Legend Of Zelda: Collectors Edition. There's probably more, I just can't seem to think of any right now.[/quote]
None of those are rare by any means. Zelda and Ikaruga are pricey and in demand, but easy to track down. BG&E and PoP: Sands of Time might be a little scarce depending on where you are, but they can be tracked down too. And of course, all three are worth owning in any Gamecube collection.
And the basketball game Ziv is thinking of is NCAA 2K3. From what I've heard, Sega had decided to stop publishing their sports game line on the Cube shortly after the game was released and didn't produce many copies.
Here's some other games I hardly ever see and have read about elsewhere:
Rally Championship
Pokemon Box
Bust A Move 3000
Star Wars Jedi Outcast: Jedi Knight II
Disney Sports Basketball
Dragon's Lair 3D
Robotech Battlecry Collector's Edition
Reprinted games that were once believed to be rarities:
Resident Evil 2
Resident Evil 3
Cubivore
Gotcha Force
Rave Master