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:
Batman (TellTale)
King's Quest
Downfall (Redux)
Oxenfree
Silence
Shardlight
Kathy Rain
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.
