I suspect the Skyward Sword first print run (with the CD) will become rare, eventually.
Some of the New Play Control games (especially Pikmin, which hasn't even broken 600,000 copies, yet is generally regarded as the superior version) are going to get relatively expensive, too.
I think, however, that, barring something like Earthbound happens, most of the games that are rare now are going to be the hard-to-find ones, and most of the games that are easy-to-find now are going to remain cheap and common.