Games in which you play as evil

[Ravinoff]

Arguably Dark Souls. The Chosen Undead is, at best, being manipulated into everything they do (which includes killing a bunch of otherwise-harmless entities) and at worst is on a campaign to actively usher in a new Age of Darkness. Don't know what I'm talking about? Read the lore on Sif, the children of the Witch of Izalith (Queelag, the Fair Lady and Ceaseless Discharge), and what exactly Darkstalker Kaathe is up to.

 

[Korskarn]

I heard Planescape Torment has one of the better evil playthroughs, although I personally never played through it as evil.

Torment is a good example. There's one instance engraved in my memory, where you can decide how to deal with an ill githzerai(think Spock elves) that asks you to end her life. You can refuse, do it yourself, or make your githzerai party member do it... you can also order him to do it in the slowest and most painful way he can, just to check if certain oath still works.
Furthermore, the game drops here and there hints that your character's previous incarnations weren't exactly pleasant people.

Torment strictly on playthrough rewards you to take the "good" options (you learn the most about your past this way), but holy shit was the Practical Incarnation ever a cold, calculating bastard.

As an example, he

Spoiler

seduces a seer to fall in love with him, specifically so that when (not "if") she dies she can act as a beacon to rescue him from the Fortress of Regrets. Similarly, he implants some goodies inside Xachacriah's intestines - while he is still alive - so that when (again, not "if") Xachariah dies the Practical Incarnation can retrieve them from the mortuary.

In a game where the player can push his Intelligence stats to be god-like, the other companions will STILL comment that the Practical Incarnation is smarter and more capable - which is evidenced in the story, since the Practical Incarnation managed to work out how to get to (and defeat) the Fortress of Regrets, while not even needing to visit Ravel, Fhjull, and Trias.

"Well..." Morte pauses. "Yeah, there's one other thing you should know - the YOU I knew before, the YOU that led us here, he wasn't like you. At all."

"The other YOU, he... he didn't care very much for anybody. For anyone. We could have ALL died in the Fortress, and he wouldn't have blinked. So... I just want you to hold on to your differences, because... well, I like this *you* better. A LOT better."

Morte pauses. "There's one other thing - I may not have liked that *other* you very much, but he was one smart basher - the smartest basher I've ever known; he always had every angle covered. If he died at the Fortress, that means... well..."

"Because whatever was waiting in that Fortress for you, chief, it already defeated you once... to this day, I don't know how you managed to survive, but if you fall again, you're going to need someone there to pull you out of that Fortress..."