A bunch of my favorites have already been listed, so I'll just mention the one that wasn't: Antichamber, a first person puzzle game that's probably somewhat like Portal in terms of how it requires you to rethink your assumptions about how space works, but it's a very different game, both mechanically and in tone. I don't want to give away too much, but it's a mix of weirdly unsettling elements (although it is by no means a horror game), a design that's actively trolling you in ways that will make you laugh, and mechanics revelations that will have you scream "Wait, I could have done that this whole time?!" It's one of those games that I wish I could delete from my memory and play for the first time again.