Note: we already did a Best Games of 2016 thread.
But if we're talking about best game played in 2016 regardless of release date, I gotta go with Invisible, Inc.! It's the most unique and challenging stealth game I've played in a long while. Never before has ghosting been so important to success in a stealth game, as direct engagement always has negative consequences. And I love how the ticking clock creates tension in a game where the best strategy is often to sit still and wait things out. And of course the permadeath makes every decision much more important. Whereas in other stealth games exploring 100% of a level or doing sideobjectives is usually a question of "can I be bothered doing this?", in Invisible Inc. there's a constant drive to achieve as much as possible to increase success later in the game, but also you know that any time you stick your neck out it might be the end of your campaign.