(For example, choosing to do something wrong makes your character dark over time).
But there is a BUT. Don't just "throw in" choices, for choices to work, you need the right game type (how you tell the story), you need the right gameplay,you need the player to feel the effects of his actions and he should care about his choices.
I personally think the original Fable is a very good example on how NOT to do it. As far as I remember, there was only ONE choice that really changed something, that was if you killed your sister or not. Also, because you always could choose between the obvious good/bad, you could go for mainly bad, throw in some good acts, then some more bad ones. It didn't affect the story in a great deal.
Also the "affecting the story" aspect is often made amateurish(like in the first Witcher), where almost all of your actions influence the last level. And even then they just influence who you fight. The fights are about equally hard.
"Heavy Rain" is a game that made choices very cool. It changed the story and didn't shy away from killing main characters if you screw up. It also didn't just add good vs. bad. You were always in a grey area and sometimes faced with a dilemma.
So, making STANDARD good vs. bad choices is easy, but as easy as they are, so generic they may feel for the player.