Bastion spoilers
There's two moments in Bastion that have really lodged in my head as game design I'm not gonna forget.
The first was the in-game achievement/reward for killing n "beasts of the wild"... which (I think for most players) was completed upon first meeting and then killing an adversarial human.
It took a goal you'd been working towards and then subverted it to show the racist, imperialist nature of your society -- without any words spoken.