There are hardly any rare GC games, and it's no trouble at all to track down copies.
Cubivore just recently got a reprint and will be in Gamestops quite frequently now for $40 "used," but it's a new copy.
Ikaruga isn't so much rare as it is in demand. You can get copies on eBay easily, and with a little diligence, it could be found at several stores.
What's rare after that? Some crappy titles no one wants like Disney Soccer or some nonsense like F1 2002 I think. You could argue the Resident Evils are rare, but it's mostly an Ikaruga situation.
Maybe the Zelda compilations are rare, but again, easy to come by.
In other words, I don't foresee Nintendo reprinting many games. It's nowhere near PS2 game rarity levels, which again have seen lots of reprints lately (Rez and Gitaroo Man, for example).