We can say many thanks to success of Wii, making it harder to find GC games used and new as many gamers discover what GC has to offer (which they missed out last generation).
IMHO, the rarest games (not necessarily the most popular)
-Goblin & Commander
-Ikaruga (should've kept my extra copy)
-PSO I&II (both original and Plus)
-Gotcha Force (still rare but Gamedude has 5 new in stock for $29.99)
-Bust-A-Move 3000 (I got the last copy sealed at TRU back in 2004)
-Spirits and Spells
-Mario DDR (I don't think it's the rarest but it was among the most popular)
-Beyond Good and Evil
-Cubivore (still rare even with GQD reprints)
-Most of Disney sports titles (not popular but very hard to find)
-Digimon Rumble Arena 2
-NCAA College Basketball 2003 (I'd hate to be a collector going after complete collection)
Some of the games are hard to find sealed and in original non PC version but by no mean rare, and I hope GQD reprints more titles (even though I collect sealed GC games). I'll visit the GQD retail store tomorrow morning, can't wait.