Knights Of The Old Republic II
Although Light and Dark side were present, they were handled very differently to the straight up press for rainbow kittens or nuke orphanage style options for KOTOR I. The choices made in that game were primarily to focus on your survival, you're constantly being hunted by psychotic Sith Lords, you yourself are a wound in the force, drawing in life around you and influencing all those who travel with you, not everything is centered on your karma. Your actions affect the way your companions look upon the world, for you, most of the options involve going out of your way to try to improve the lives of those around you, of course, these means you'll spend a lot of time focusing on others rather than yourself. Or you can focus on getting stronger quickly and allow others to struggle for themselves.
Examples such as the fight within the palace at Onderon, depending on who you picked to help, do you aid the soldiers fighting by risking loss of energy and vitality, or do you conserve your strength to face your own greater challenges.
Then there are a lot more complex moments, such as a beggar on Nar Shadda, who won't leave you alone until you either threaten the man with violence or hand over some credits, yet either of the actions results in suffering, such as the man running in fear but attacking someone else for money, or he is attacked for his newly gained credits.
Plus there is a great sense of motives within the story, of course there are some straight up good/evil choices, but those usually tie in well with the main story, and usually branch out, rather than asking you to simply save a child or set it on fire, you might be given the choice, such as, to aid the Jedi Masters who cast you out, as well as recieving some rather crucial knowledge. Or perhaps you would rather have revenge for what you believe they did to you, you'll tear what you want from them, but the further down the road, more and more will turn their backs on you.
In a game like KOTOR II, you can't simply save everyone, you can't please everyone, even the smallest decisions affect the outcomes of so many lives, the Exile's complex background ensures that it's never as simple as being the next Jesus/Hitler. All of your choices have benefits, consequences, branches and complex morals and influences rolled up into one.