The Grunts and Brutes in Amnesia: The Dark Descent. The Grunts have grotesquely distended mouths, stretching all the way to their chest and past the sides of their heads. The Brutes, on the other hand, don't even have faces - their heads are ripped up masses of flesh with teeth protruding in random places and a single eye somewhere within.
If you get stung by wasps in any game of Animal Crossing, your face will be noticeably affected, with one eye swollen shut, and the other swollen halfway. Talking with any of your villagers in this manner has the chance of frightening them, as they might mistake you for a monster, before their fright immediately turns to sympathy.
Once again, Two-Face. The damage done to his face is particularly gruesome here, much like in Nolan's films.
Scarecrow's design in Batman: Arkham Knight displays this as well. After Killer Croc mauled the guy in Batman: Arkham Asylum, Crane is implied to have had to reconstruct his own face, with gruesome, terrifying, and undead-looking results. It's impossible to tell the difference between grafted-on burlap and actual flesh.
Batman: The Telltale Series has Two-Face once again, this time with his injuries caused by the Penguin in the climax of Episode 2 if the player chooses to help Catwoman instead of Harvey. His injuries look similar to those from the Nolan films, but with the added horror of continuing to fester and bleed long after.
In BioShock, the villainous Andrew Ryan is one of few non-disfigured people left in Rapture, having forced the entire population to join his super soldier army - a process which entails insanity, cancerous growths, and facial disfigurements. In the last quarter, the player repeatedly bashes his face in with Ryan's own golf club. Ryan ends up looking not unlike the "splicers" he created and sent after you.
Concept art for BioShock Infinite depicted that traveling through tears could result in the traveler being merged with versions of themself from the past, future, or alternate timelines, resulting in various facial deformities.
The backstory for Our Lady of the Charred Visage in Blasphemous involves this. The people of her village worshipped her for her beauty, to the point they were praying to images of her face instead of the Miracle. Horrified at the sacrilege, she poured boiling oil on her face and joined a convent, but her burn scars never healed and never stopped smoking. You fight her as a boss, and the effects of the oil are all too apparent.
Handsome Jack from Borderlands 2 wears a mask modeled after his original face because, as revealed in Borderlands: The Pre-Sequel!, after receiving a vision from a relic found in the Vault of the Sentinel, Lilith blasted it and branded Jack's face with the Vault symbol it depicted. It also destroyed one of his eyes, so his mask has a prosthetic eye attached to it.
Comedic example in the Mad Moxxi's Wedding Day Massacre DLC, where completing the campaign awards you with a head customization item that pulls off the player's face exposing their skull to mimic the Goliath's exposed head. In the case of Zer0, it reveals that he's robotic underneath but amusingly is called "N0t C4n0n".
In Tales from the Borderlands' fourth episode, Rhys needs to scan Vasquez's corpse to make a disguise. When he gets back to where the body is, he finds Psychos have quite literally cut the face off the body, and ends up having to sneak through an alley full of sleeping Psychos to figure which one of the face-thieves is wearing Vasquez's stapled to his mask.
Exaggerated in Brain Dead 13: If Lance can't escape the Beautifier in Vivi's Salon, the mechanical powder puffs will close in on his head, screw it up, and turn it into a skull!
Catherine: The boss of the Clock Tower, the Child With a Chainsaw, is a cybernetic version of the earlier boss monster the Child. Its face is covered in mechanical panels that open up to reveal a particularly horrifying visage, as seen when it tries to stop Vincent from escaping at the end of the level.
Near the start of Dead Space 2, a man is transformed into a necromorph right in front of you. It's not pretty.
Much like most of the other body part horrors, this can be easily inflicted in Dwarf Fortress. With enough wrestling skills, you can easily hold your opponent down by the head while you systematically pinch and gouge their facial features to your leisure.
The various kinds of enemies in The Evil Within all suffer from this. Ripped off or shredded flesh, gaping holes in the skull, impaling glass or metal struts, barbed wire wrapped tightly around the face, or any combination thereof, are all in vogue. One particularly rare and nasty substrain capable of invisibility has had its face... "peeled out" to resemble a writhing nest of tentacles, making them look somewhere between an open wound and a cthulhumanoid.
Ull, the chieftain of the Udam tribe in Far Cry Primal has a melted nose and ears, and exposed cheek muscles, due to getting injured by Izila fire arrows in the past. It makes him look inhuman.
Facial horror is a motif in FAITH: The Unholy Trinity. Most notably, Amy, the possessed girl whose exorcism starts the plot, doesn't have one, instead having a red hole that an arm reaches out of partway through the fight. It turns out there's more to this than just a recurring theme. In this universe, one can open a portal to Hell by inflicting the Second Death on someone. This is done by carving their face off and then shoving a live infant into the hole. Something about Amy made her the perfect candidate for the Second Death, and most of the plot of Chapter III involves preventing the cult that did this from getting its hands on her again.
The original Five Nights at Freddy's game has the main character's eyes popping out of the Freddy suit he gets stuffed into on the Game Over screen, as well as a certain Easter Egg in which a poster changes to depict Freddy ripping the top part of his head off.
Five Nights at Freddy's 2 has Withered Bonnie, who completely lacks a face save for a lower jaw and two faint lights serving as eyes.
And then there's Springtrap from Five Nights at Freddy's 3. In two rare bootup screens, you can see a human head inside him, with two large eyes jammed into its sockets, hooks being dug into its cheeks and its mouth speared open and lacking a few teeth. It also completely lacks a nose.
The entirety of the Five Nights at Freddy's: Sister Location animatronics can count as this, as each of them has multiple faceplates that open and close to expose their endoskeletons, which is especially prominent in each Jump Scare.
The main antagonist of Hitman: Blood Money, Alexander Leland Cayne (also known to players as Jack), is an Evil Cripple with a motorized wheelchair and a half-flayed face. His left eye is also a discolored yellow.
In Let It Die, the first boss is a twisted handyman/hardware seller/gang leader with a beard made of screws and his arms stitched on his temples. According to the "Tales of Barbs" info, he rams a screw through his jaw every time he destroyed a rival gang.
Lobotomy Corporation: In the Legacy version of the game, Little Red Riding Hooded Mercenary would take off her mask while pursuing the Big and Might be Bad Wolf. Players can see why she keeps her mask on: She is missing her skin, her teeth and one of her eyes.
Lunacid: The mummies found in the Temple of Silence have a massive cavity above their nose, looking like someone scooped out their brain through their face.
The very appropriately named boss The Nightmare from Metroid Fusion starts off with a face resemblingFrankenstein's monster, which gradually falls apart in the most disgusting way possible as the fight progresses. To wit, green goo comes out of its eye sockets, running down to its chin. Then the surface comes off, revealing goo everywhere and what look like four more eyes higher up! Then the whole face starts melting away to the extent that one of the eyes nearly falls off!
One of the antagonists of Middle-earth: Shadow of Mordor is the Tower of Sauron. The lower half of his face looks necrotized, and he wears armor that shows off his skeletal mouth.
In the same fashion, this can apply to some of the UrukCaptains you can encounter, thanks to the Nemesis System. Uruks with faces distorted by cancerous-looking pustules, or facial scarring, all the way up to having their entire head wrapped in a bag from the injuries Talion inflicted on them.
Sheltem the Dark from Might and Magic has a classic Two-Face appearance under his helm. Since he's an android, keeping it that way seems to be a deliberate choice.
The Emblem Curse in Innocent Sin. While not explicitly shown in the games, as all students that have it cover their heads with bandages, the anime trailer shows that their faces are literally melting.
Tatsuya Sudou in both parts of the duology gets half of his face burned off (and loses his eye in the process, both times). He's pretty incensed about it.
Persona 5: When characters first awaken to their eponymous Personas, they have to rip off masks that are part of their faces, causing blood to erupt as they for all intents and purposes rip their own skin off.
Propagation has the human-spider hybrid whose face literally splits open, revealing a flesh-coated skull. That it bares in full glory while chasing after you!
The Brute from Paradise Hotel can be damaged by shooting it's head, causing it's facial skin to peel off. It doesn't stop the monster from trying to chomp on Emily.
Quake: Most monsters in this are set with giant mouths for faces.
Resident Evil 2 (Remake) has Sherry become infected with the G-virus, which causes sickly looking veins radiating from her left eye while said eye also turns yellow. This wasn't visible in the original game due to the graphical limitation of the Playstation.
Nemesis from Resident Evil 3: Nemesis has brown, rotting skin, his lips have been pared back so there's a permanent grimace on his face, his nose is missing, and one of his eyes is gone, with a row of staples running down from the top of his head across the empty socket.
In Resident Evil 4, the Novistadors can melt Leon's face off with their acidic vomit. In the Japanese version, decapitations were replaced with facial disfigurement.
In Resident Evil 5, the Majini get progressively more disfigured as the game goes on. The tribal Ndipaya, in particular, look like they've chewed their own lips off.
Resident Evil 6 The various J'avo encountered in the game all have significant facial deformities, ranging from lesions and cuts to multiple eyes in asymmetrical arrangements. In the case of Derek Simmons, there are his virus-mutated form's first two stages, in which the skin and flesh on his body shift about on his body like Jenga pieces, letting one see his skull underneath.
The titular character of Sally Face had this happen to him when he was a child, presumably as a result of a dog attack. We don't know what exactly happened to his face (apart from losing an eye), but he had to wear a prosthetic face ever since. In the flashback, his face right after the attack is covered in so much blood that it's impossible to tell.
Salt and Sanctuary has Lenaia, the Queen of Smiles. Her epithet as Queen of Smiles was earned by her habit of cutting a Glasgow Grin into the faces of the many, many people she had executed for increasingly frivolous and nonsensical reasons before hanging the corpses up as decoration. When her reign was finally cut short by a mob of vengeful villagers, it was seen fit to leave her with "the greatest smile of all." By the time you fight her in the game, she's a rotting corpse with a mess of gore where her lower jaw should be.
In Star Wars: The Old Republic, Arcann's face was disfigured in his campaign against the Republic and Sith Empire, and most of it is obscured by a broken metal mask as a result. He gets rid of the mask when he becomes The Atoner.
Several cosmetics in Team Fortress 2 follow this. One, in particular, is the Medic's Second Opinion, which gives him a discolored skin graft on the left side of his face that is also a malevolent Split Personality (well, more malevolent than normal Medic).
No-Face in Twisted Metal: Black had his eyes and tongue removed and his eye sockets and mouth stitched up (the manual explains that he sees through telepathy) by a Back-Alley Doctor who lost several thousand dollars betting on him in a boxing match. His story ends with him about to return the favor via Extreme Mêlée Revenge.
In the 2012 reboot, Krista Sparks/Dollface receives a small cut on her face, which her mind envisions as a monstrous necrotizing infection over her entire mouth, leading to her getting her White Mask of Doom to hide it.
While this is, of course, apparent for various zombies, The Walking Dead: Season Two takes a step further with the death of William Carver, who has his face savagely beaten in by Kenny with a crowbar. The end result is... not pretty to look at, as a lot of his skin is peeled off with his broken skull showing underneath. Those who are more squeamish have the option to skip this scene, at least.
Waxworks (1992), having tons of nightmarish death scenes, and many of those showing only your face naturally has tons of this. Particularly the plant mutants in the mineshaft, who will claw/melt your face off, if you're lucky. In fact, the picture at the top of the page is from this game.
In XCOM 2, the ADVENT soldiers are supposedly human, but actually underwent genetic manipulation that had the effect of altering their facial structure to resemble a mix between human and Sectoid. Their helmets conceal these disfigurements, only revealing their mouths, the one part of their face that still looks passably human.
◊ is from Splatterhouse 3. This is your terrifying punishment for failing to save Jennifer in time. Oh, and DON'T LOOK THIS UP AS A VIDEO. The music will freak you out.
