The 3 games I can think of where choices affect your alignment are:
*Shadow the Hedgehog
You can be a total prick in each level but ultimately he saves the day anyway when you unlock all the endings. All Shadow does in each level is constantly remind the player who he is and in some endings, he turns into a complete maniac. In-game graphics are sub-par, but cutscenes are eye-orgasmingly beautiful. For a PS2 game.
*Infamous
Again, gameplay is choice based and you unlock abilities depending on whether you'rea a White Knight or a total cunt. I think Infamous 2 is pretty much the same.
*and the Fable series
Never played them myself but a
review by Yahtzee was enough for me.