Sneak 'n Stab.
I'm not usually into playing a lot of games where stealth is forced upon you, which is slightly odd because if a game like Dishonored comes out I tend to use the stealth route instinctively. Anyway Mark of the Ninja is pretty great. It's really thought out it's stealth mechanics in a really clever way where things like enemy vision is very obvious and if you're in the light or dark is immediately apparent. The action of killing people stealthily where you have to drag the mouse in the right direction isn't great, it works sure, but it's kind of awkward to do on a mouse. I didn't check for gamepad support but given that it came out on 360 first I'm going to guess that it's all in there and works fine.
I haven't played that far but it seems like there are quite a few tools you can use to get back out of sight if you mess up. You take a pretty hefty score penalty if you do so and if you're looking to leaderboard chase it'll probably cause you to restart but the game has really good hooks between the high scores and the seal system to encourage you to do pretty specific things during levels. It also seems like there are challenge rooms which are a bit more puzzly than the normal game which make for a good pace but they're pretty hidden away so it's hard to say how many you would run through if you weren't exploring too much.