I have to disagree with Okami. Honestly even Psychonauts is more of a sleeper hit than Okami and that's the definition of a cult classic (hell it's too popular for that classification too). God, I remember when the game first came out. It attracted weeaboos like flies to honey. Definitely not saying it's a bad game though (I got so sick of the oversaturation I just avoided anything to DO with that game so I still haven't played it).
Anyway, instead of making a huge ass list (lord knows I could), I'm just gonna mention my prolly biggest one and that's Majin and the Forsaken Kingdom.
An adorable game, kind of similar to Ico or The Last Guardian in that it's sort of an escort/partner-up-with-a-monster-thing kind of game, but no where near as... uh, heavy in atmosphere, I guess (I'm tired, shut up). Well I enjoyed it anyway. I can count on one hand the number of people I've talked to ONLINE who've played it, forget irl.