9. Spec-Ops: The Line
Spec-Ops: The Line is up first because it has perhaps the most famous "you've been the bad guy the whole time" twist in gaming, to the point where more people probably know about reveal than have actually played it.
It's so effective because of how it uses gameplay mechanics that all third-person shooters utilise to subvert player expectations and build to the reveal that they're actually controlling a pretty bad dude.
Of course, the biggest example of this is the infamous white phosphorous sequence, where the player is encouraged to bomb "enemies" from the sky like they've done a thousand times before in the likes of Call of Duty. You don't even question it, but the consequences of your actions are revealed when you have to walk through the environment you've just decimated, and gaze upon the corpses.
And it's only then when you realise they were innocent civilians.
After this it's also revealed the villain is already dead as well, and your character's fractured psyche has hallucinated an evil antagonist to excuse his (and the player's) actions.