Mega Man Legends 2 and Tronne Bonne were my first thoughts. I was surprised to be able to grab Ghost Trick, MM, MMX and MMZ collections for cheap (PS2, PS2 and DS respectively) recently. Ghost Trick I figured would have gotten a low print run, was very glad to get it cheap.
Not sure I'm surprised since lolprintruns, but the high price of Folklore is a travesty considering it's situation. It's not THAT old, for a system still supported, yet has no digital copies and is quite expensive to get your hands on, game deserves better than to be ignored for price. I have a copy, but it still makes me sad.
Plenty of Nintendo games.
Like, Metroid Other M is $80. Wtf?
You can also still find some DS games that are $40.
You can get Other M for dirt cheap. New prices for old games aren't always indicative of value, especially not in physical stores. It's $15 new on amazon right now.