Well, a new Thief was just released last year. And you have the Assassin's Creed series.
Although it's a little bit older, I always liked the SWAT series (at least SWAT 3 & 4). Although they're an FPS series, the focus is more on arresting the criminals than just shooting them in the single-player mode (and let me tell you, it's a lot easier if you're sneaking up on them than if you just run in guns blazing). And the multiplayer servers tend to have a lot of game variants that emphasize sneaking around and non-lethal weapon choices (nothing like being on a VIP Escort server & being the idiot Red Team shooter that puts a hole through the VIP for the loss, & being forced to take a taser & beanbag shotgun for a round...).