Mine is Dreamfall Chapters for sure.
I know most of it came out last year, but I don't count an episodic game as belonging to a particular year until all of its episodes are out. So for me, Chapters is a 2016 game, and I consider it one of the best games I've ever played.
My Honorable Mentions are:
I haven't played much of Yesterday Origins yet, but so far it's really good and will probably be added later.
I also really enjoyed Deponia Doomsday, but my Honorable Mention list is way too long as it is.
All in all, I think it's been a fantastic year for games.