MILD SPOILER ALERT. There, you've been warned.
Finally got around to playing this, and wow. The dark humor may be a bit over the top, but for me what really did it was the catastrophic collapse of the fourth wall, and then the wall behind that: the highest moment was easily, "This little endeavor isn't for you. It's for me"—interestingly on only one path through the true ending, and fortunately the one I chose first.
I'd say this game's deep commentary on our inability to change has given me a lot to think about—enlightened me, even made me a better person—but then, reflecting on its message, I suppose I know better. We are all Merkle: if you come away from this game thinking you've learned something, you haven't, and yet if you think you haven't, you have. This game is a koan.