Mark of the Ninja

you forgot to add Bad Rats to that list :(

Payday 2? It has a few missions for stealth and afaik it has native controller support

Metro 2033 and Metro Last Light have no-kill styles/achievements, and controller support.

Not sure if Not The Robots has full gamepad support, but I think it's worth a try.

recently i was playing alpha protocol .... good game and you can do stealth but not 100% there are some boss fights that you need to go loud + you have to play it with controller pc controls sucks .....

i think you can do deus ex HR stealthy too(not sure 100% cause i haven`t finished the game yet) and i think it has native controller support...

Stealth Bastard Deluxe. I played it with a controller, and that's the way it was ment to be played. Also it even has stealth in the tittle.

My brother picked up Styx a while back. I don't think he's played it yet, but it looks pretty cool!

Styx : Master of Shadows

It's a really good infiltration game and it has full controller support.

Edit: GNordell beat me by 1 minute. Thank you for the help bugzkilla, I always forget how to do it.

Splinter Cell Games

You could include the Tom Clancy's Splinter Cell franchise. The first two games (I believe it was called Pandora Tomorrow and Chaos Theory) were so stealthy that you would automatically fail the mission if you fired your weapon or got caught. I don't know if you would consider the Chronicles of Riddick franchise purely stealth, but majority of the game involves staying in the shadows.

Hope I was a little help.

Fallout 3 and New Vegas I guess ᶘ ᵒᴥᵒᶅ

Got 3 that I remember playing with a controller, and i'm not one to install extra apps to enable playing with controllers so i'm guessing they all have native support:

Metro Last Light includes the possibility of a stealth run, I think there where just a few small levels where you couldn't really go the stealth route but the game does have a lot of achievements related to completing levels without raising alarms + the "Shadow Ranger
Complete the game without killing any Humans unless forced to." achievement.

State of Decay could be considered a stealth game as well since you can actively avoid zombies by sneaking but imo the balance isn't right and it's easier to just bash your way trough the game.

Splinter cell blacklist, I haven't gotten around to try this one myself but I do remember doing some research on it to make sure I could play it with a controller, seems like it does have support yet it isn't listed as such on steam.

Edit: Wrong thread.