In AdventureQuest Worlds, a thinly-veiled parody of Good Angel Bad Angel is represented by the "invisible" twins called Xing and Xang. Xing dresses like a complete Emo Teen and Xang dresses like a stereotypical angel. Their job is to "guide" the heroes, but they don't listen to advice in the cutscene — at least until Evil Overlord Drakath switches Xang with her Chaotic Evil twin in the Mirror Realm.
The god game Black & White also has a Good and Evil Conscience (an old wise man and a wisecracking devil) to give the player advice and color commentary.
In The Legend of Kyrandia: Malcolm's Revenge, the titular Villain Protagonist has both an evil conscience named Gunther and a good one named Stewart. The latter is crushed under a rock during Malcolm's childhood as part of his Start of Darkness but returns in-game. Malcolm then asks the player to choose which one to stick with or to chooseboth since Malcolm himself doesn't care about morality, just wanting to Clear His Name so that he can finally go home and take a nap.
A brief scene in the second Simon the Sorcerer game features this trope. Simon being Simon opts to side with the bad angel.
In Mass Effect, there are several instances when Commander Shepard must resolve a situation by choosing between a clearly good Paragon option or a clearly evil, or at least ruthlessly utilitarian, Renegade option. In some of these cases, Shepard's two squadmates will offer their opinions on which option Shepard should choose with one squadmate supporting the Paragon option and the other supporting the Renegade option. There is even a hierarchy in 1 to determine which character will support a given course - Kaidan will always support the Paragon option; Liara will support the Paragon option unless your other teammate is Kaidan; Tali will support the Paragon option unless your other teammate is either of the above; and so on down the line, until you get to Wrex, the most Renegade option available.
The Suffering used a variation of this trope. When Torque is faced with a moral decision at some points, his wife Carmen acts as the shoulder angel and Torque's evil side acts as the shoulder devil. The sequel has Carmen act as the shoulder angel and Blackmore act as the shoulder devil. In both games, they do not actually appear at Torque's side at these points, but their voices can be heard.
The Pyro has this as a Misc. Item: The Cremator's Conscience; they are in a chest pocket. Description: "'Burn him with fire!' 'No Burn him with fire, then hit him with an axe!'"
inFAMOUS 2 has the characters Kuo and Nix, who each encourage Cole to act towards good or evil, respectively. The subversion? The climax has them switchroles.
The turn-based RPG iOS game Devil's Attorney, which centers around an attorney with little respect to the law or reality, at one point shows a tiny version of the hero in a devil costume floating over his left shoulder. When he looks to his right, a second, identical devil appears.
The title character in Fabulous: Angela's Sweet Revenge has little floating balls pop up after her husband offers to drive her boss home from work. The yellow one with a halo says that a marriage should be built on trust and the red one with horns sings a bar of "Suspicious Minds."
Catherine uses this method to display the hero Vincent's mental morality as the game progresses, and whether he chooses Catherine or Katherine by the end of the game. At certain points in the game, we hear Vincent's thoughts on the current situation, and they change by having either an angelic cherub or a demonic cherub egg him into their way. Unlike most cases, they don't represent good/evil, but rather order/chaos.