Since hardly anybody brought up any DS games I would have to say all the Castlevania games on the DS. Also I put in another mention for Crackdown and even though I really don't like FPS I thought Condemned 2 was pretty good and definitely qualifies as a hidden gem and so does Infinite Undisovery.

Hidden gems, is a bit tricky. For instance, Catherine I wouldn't really include Catherine as hidden gem because it was done by the P3 and P4 team, and was expected to be good. If you're going by games that don't sell I could list a lot.

My criteria is games that were unexpectedly good. But even then it's difficult. For instance I'm not sure whether to include TWEWY. I wouldn't have expected a game by the people who developed chain of memories to do my favorite JRPG. But, I wouldn't have been surprised that Nomura was heavily involved with great music from the dude who did crisis core.

Legend of Hero's Trails to the Sky
Spec Ops the Line
TWEWY
Binary Domain
Lara Croft and the Guardian of Light (Again, I would expect a CD game to be good, but not a game that felt like it was going to be a throwaway).

Enslaved: odyssey to the west
And
Vikings: Battle for the asgard. Really play this game, it's amazing and the battles are epic!!

Valkyria Chronicles (the original).

Endless Ocean 2 and Xenoblade.

I thought it always had a physical release?

Enslaved: Odyssey to the West

Alan Wake

I have not played every game to be able to tell, but the one i can tell is a gem and was incredibly belittled by western press when it should have been hailed as a masterpiece is: Nier. There is no other game like it.

A lot of people saying Alan Wake here. Is that really a hidden gem? I mean I know it didn't quite hit the sales mark they were hoping (and frankly deserved), but it's still a fairly well known game.

Anyway, Alan Wake was my favorite game of this entire gen