BioShock, The World Ends With You, and KotOR.
Also, the MGS franchise. Though I've always been wary on the plot twists of the franchise, because sometimes they take it a tad too far. MGS did a pretty good job. MGS2's ending made my brain have a minor implosion. I'm freaking serious. I couldn't think straight for days.
MGS3 did it better, though... Having a good plot twist but it doesn't overdo it. It's not as big as any of the other games, though.
MGS4 /almost/ went too far, but it landed about a centimeter away from going overboard with it. So I thought MGS4's was perfect. Though my personal favorite twist of the franchise is the one(s) in chapter 3 of MGS4.