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.
Angela Napoli in Fabulous series has little floating emojis (pictured above) pop up as a Running Gag. For example, in Fabulous: Angela's Sweet Revenge, the yellow one with a halo would say that a marriage should be built on trust, while the red one with horns would sing a bar of "Suspicious Minds". As of Wedding Disaster, they are now represented as miniature versions of Angela herself.
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.
The Secret World begins with an encounter with these: after first being chosen by one of Gaia's Bees, you have a dream about meeting two members of the Host - one a Grigori, the other a Nephilim: the Grigori wants you to choose for yourself and avoid being corrupted by the voices that whisper in your sleep, while the Nephilim wants you to "make the right choices" and follow the will of the voices. They crop up again in the finale after you decide on what to Dreaming Prison.
Randal's Monday: Randal gets one of these scenes at Mel's Pawn Shop on the first Monday. The good one is Matt, and the bad one is Marconi. When Matt understands that Marconi will impale him if Randal doesn't sell the ring, he quickly tells Randal to do it.
Joker: It didn't feel great, you know? Stealing from her. Like it was a little Harley with a halo on this shoulder telling me not to do it, and then a bat on the other whispering, "Just get it, John." Or did you have the halo and Harley the horns?
Soriz of Granblue Fantasy comically has them for being a Dirty Old Man. They pop up during his SSR training, the good one urging him to continue his training to find his own philosophy, and the bad one trying to make him give up and go back to fooling around. They eventually start arguing so loudly that Soriz ends up beating the crap out of them, giving him the final push he needed.
At the end of The Spectrum Retreat, Cooper and the manager take the roles of the two angels, urging you to either leave the simulation, or wipe your memories and remain. It's up to you to judge which is the good and which is the bad, though.
Astra Superstars: Invoked in that two sub-boss characters are named "My Devil" and "My Angel" who represent each characters' darker and better qualities respectively. To quote the other wiki: "Depending on what is said, the player can encounter the Devil (based on bad judgment of character) or the Angel (based on good judgement of character) to fight before the final boss, though the Angel requires the player to judge their opponent well and not have any hiccups, or else the Devil will inevitably show up, should just one choice be bad."
In League of Legends, Tristana's Little Demon skin changes her recall animation to one where she has Little Devil Teemo as her devil whispering into her ear and a similar-looking Teemo in a halo and white robe as her angel. She grabs the latter, throws him into the air, catches him in her cannon and shoots him offscreen in a spray of feathers.