I think that Zero Escape: Virtue's Last Reward (as well as the game to which it's a sequel, 999 on the DS) deserves a fair mention. It's a pretty popular locked-room puzzle game with a neat story, but it doesn't get the same kind of exposure that Mario and Pokemon get. It may not be the kind of thing you're looking for, but considering it hadn't been suggested yet, I thought it was at least worth pointing out an often-overlooked yet interesting game.