Braid
I played some of Braid when it came out on XBLA, on a friend's Xbox, up through the third world. Months later, when the PC version came out, I played the first world again in the Steam demo - then once more when the Mac demo was released. I still loved the game's crazy blend of platforming, puzzles, and twisted metaphysics; but having become so well acquainted with it, by the time I actually sat down to play the game in earnest, the last thing I expected Braid to do was blow my mind.
Then I got to the fourth and fifth worlds. Holy fuck!
My brain gasped for mercy. It was all I could do to whizz through the levels, for the sake of coming back and solving the puzzles later. I told myself I would put it down and go to bed, but the "Just one more puzzle" sensation drove me all the way to the attic. In retrospect, it makes the game feel short - but the past few hours have been some of the most dense and awesome of my entire gaming career.
Even now that I've got a solid handle on the gameplay mechanics of the first five worlds, I'm still turning over in my head the notion of how all this was programmed. Each in-game entity must have its own sense of "forward" and "backward" time, what can trigger it to move (or stop) in each time-direction, and how quickly - and the procession of time in the game, as an abstraction of actual time...
This is going to keep me up all night.
Progress: Final (?) world