Phoenix Wright: Ace Attorney - Dual Destinies has the mysterious villain known as the phantom, an emotionless assassin who can perfectly disguise ???self as anyone; he/she/it has done this so many times that the phantom has actually forgotten who he/she/it really is, and in the end suffers a .
Darth Revan, whose face is masked during flashback scenes to hide the fact that the player character is Revan him/herself, having been memory-wiped by the Jedi and put into the service of the Republic.
Darth Nihilus in the game Knights of the Old Republic II, whose face is obscured and who speaks only in an incomprehensible series of tones. In a partial subversion of the trope, Nihilus is unmasked after his death, but his identity is not revealed to the player; depending on how the game is played, he is described either as "Just a man, nothing more", or something along the lines of "infinite darkness" before his body inexplicably disintegrates. The one who saw his body was his blind apprentice who "saw" things through the Force.
Mandalore, in the same game series, is a subversion of the trope; as Canderous Ordo, the character is a member of the party in the first game and makes no effort to conceal his name or face. By the time the player meets him in the second game, however, his entire body is concealed by a suit of armor that he refuses to remove and he does not acknowledge his real name.
TO clarify, in lore Mandalore isn't a person so much as an idea. Hence the faceless-ness and refusal to acknowledge his name.
Illegal street racing games seem to thrive on this trope. Need For Speed Pro Street even goes so far as to make the player character wear a full-face helmet.
In other NFS games, the PC's face is blurred/pixelated.
In Guilty Gear, a certain non-playable character is referred to only as That Man, on top of which his face is constantly in shadows for no readily apparent reason.
Faust from Guilty Gear X onwards has a rationale. He constantly wears a paper bag over his head to hide a previous identity he'd rather not be remembered for. This identity is strongly implied, but never directly stated, to have been Doctor Baldhead, the homicidally insane playable character from the first game in the series. He removes the paper bag in Guilty Gear XX during May's storyline, but you still don't see who he is due to his face being shaded. The only thing you can really tell is that he's bald — made obvious by the bright light shining off his head. He apparently only does it to freak May out, as she claims to despise (and appears to fear) bald people. Things get hairy. Or rather, they don't.
Super Robot Wars dabbles in this a lot, usually replacing a character's portrait with a ? and ???ing out their name. Sometimes, they make fun of this, such as in MX, when their shadowing technique was to only partially shadow someone's face, so its really obvious who they are. At one point an EVA Monolith is partially shadowed out, but you can still see the words on it that say who is speaking through the monolith. In addition, Mooks virtually always have their face above their nose obscured, either by a helmet or shadows in place of their eyes.
Meta Knight from the Kirby series. He will challenge Kirby to a swordfight, and when defeated, his mask is cleaved in half. He is briefly revealed to look very similar to Kirby, before wrapping his cape around his face and vanishing.
World in Conflict does this with the main character, Parker, which represents the player and isn't defined at all with the exception of his name and rank. He appears in cutscenes, but always has his back to the camera or something blocks out his face. The game also features a name- and faceless president.
Halo - Master Chief's face, hidden behind a face mask and clever camera work, is a source of debate among fans. This was because, despite having a voice, and "personality" they wanted to keep an active AFGNCAAP factor going. In the novels, Master Chief does take off his helmet occasionally: he's described as being deathly pale from spending so much time in his armor, and having brown hair and eyes. Halo 3: ODST and Halo: Reach also have protagonists who never remove their helmets. Reach also has one NPC squad member, Emile, who never removes his helmet (which has a skull etched into the front of it) either.
In Halo Wars, all the marines except Sergeant Forge wear balaclavas, and the Spartans never take off their helmets.
In the epilogue of Halo Reach, the dying Noble Six removes his/her damaged helmet, but you still don't see his/her face.
At the end of Halo 4, the screen goes black just as the Chief's helmet is taken off. This is halfway averted in the Legendary ending, where you get a brief glimpse of the area around his eyes (though the eyes themselves are shadowed out).
Oki from Ōkami wears a bear mask at all times, in fact every denizen of Wep'keer Village wears an animal mask. The imps wear simple white paper masks as well and when Amaterasu dons a similar mask, she's accepted by them to be an imp, despite obviously being a wolf.
Shiki from Tsukihime, with the exception of the prologue (when he was a child). Since the game is told from his perspective, this makes sense; he only shows up on-screen during unlocked images, but never with any detail above his mouth. This only holds true in the original Visual Novel (not the sequel games, anime, or manga).
Many Visual Novels in general tend to do this, usually via blinding bangs, Tsukihime was just following the trend. Apparently, they do this so that the player can imagine himself as the protagonist. However, the Nasuverse expanded and got more complex, Shiki needed to be a complete character and so he was given a face.
Captive: Throughout the first mission the player has faced gunslingers in samurai-like armor (don't ask) that have the face of an orc, an insect and a skeleton, in ascending order of toughness. In the second mission, it has no face at all. The fact that it was armed with a pretty dang powerful flamethrower didn't help.
Jack of Blades, the Big Bad in Fable, always wears a white and red mask. In Fable: The Lost Chapters, it's revealed that Jack is a body surfing ancient entity that lives in the mask itself, who's moved from age to age by possessing the various dumb schmucks who've put the mask on.
In Fable II, the Wraiths are examples of this trope. These are floating spirits who summon ghostly children to attack you. They also mock you with revelations about your past and mistakes you have made.
The Dark Savant, Big Bad of the last two Wizardry games, wears a face-concealing helmet at all times.
Battlefield 3 plays this trope straight with Corporal Miller and averts it with Staff Sergeant Blackburn and Dima, albeit Dima's face is revealed when you switch to Blackburn for the end of "Kaffarov," which had mostly been Dima's level and in the ending cutscene.
Semi-averted in most of the Half-Life games, wherein you don't see what the P.O.V. character looks like and there are no mirrors anywhere in Black Mesa, but the protagonists are shown in the box art... except Cpl. Shepherd in Opposing Force, who wears a Black Ops-style mask there.
Fallout 3 DLC "Operation Anchorage" allows the character to command a squad of men- each one seems to wear a full face balaclava that means every one looks exactly the same (the same applies for the Chinese soldiers you fight against, and for the player character in the similation). This trope does not appear in the main game, though.
We never see Vile without his helmet in Mega Man X. But being a robot, the helmet could very well be his head. Its never clarified.
In Mega Man Zero, X's "face" is just a ball of light, since the Big Bad in the first game is a clone of him and looks exactly like him, save for the red eyes, and from the sequel onwards his face is always obscured by light in the dialogue boxes. Ditto Omega: he hides his face with armor, to set up the reveal that his real face is that of Zero, since this Omega is possessing Zero's original body.
In Dead Space, Isaac Clarke's head is completely concealed by his helmet throughout the whole time you play as him. His face is only revealed in the ending, and also in the game's intro, if you use the analogue sticks to fiddle with the camera angles. This is averted in Dead Space 2 - although he still has his helmeted suits, he is often shown with his face on display.
The Dynasty Warriors version of Wei Yan is always portrayed wearing a mask. A cutscene in Dynasty Warriors 4: Empires shows Wei Yan's mask accidentally getting knocked off. He's only shown from behind, and the other characters react with shocked horror. Pang Tong, meanwhile, wears a veil that obscures his face from the eyes down.
Pang Tong's is a more justified example, as in the novels, he was portrayed as being ugly. Despite his major contribution to deflecting the Wei forces at Chi Bi, Sun Quan refused to hire Pang Tong on the grounds that he was butt. Though Liu Bei took him in, he supposedly was not a Pang Tong fan, either.
The player character of Pokémon Stadium has his eyes hidden by a hat similar to Red's hat and Ash's original hat. Oddly enough, he is the only faceless protagonist in the series.
We never see any Cubone and Marowak without their skull helmets, either.
Caster in Fate/stay night, played for an ambiguous and mysterious enemy. You can see her mouth, chin and lower cheeks, but most of her emotions have to be expressed through body language. When the hood finally falls off, it's revealed that she's actually incredibly beautiful... too bad she just skewered and is bleeding to death, hm?
Taokaka and the rest of the Kaka clan from BlazBlue wear hooded jackets that show nothing of their face except glowing eyes — red, for Taokaka — and a mouth full of sharp fangs. They probably look like normal catpeople under the hoods, though. Probably.
Most games in the Dating Sim genre have a very generic, if not completely faceless, look for the main character so that the player can project themselves into the game. This extends to the animated adaptation of some of them: Sentimental Journey, for example, the protagonist isn't even named.
The Nancy Drew game Danger By Design features an eccentric fashion designer who's begun wearing a mask all the time. Solve the crime, and you earn The Reveal that she's hiding a really stupid tattoo on her cheek.
Helba is always shown with a crown/mask covering her eyes. Her full face is shown in XXXX, but the XXXX series is not considered canon
The same goes for Morganna. Whether she even has a face can be called into question, since she is The World itself. Every phase does have an eye located somewhere on its body, and this is commonly believed to be Morganna's eye watching through her phases. Again, in XXXX her face is somewhat shown, but these books are not considered to be canon due to their constant clashing of the original video games and plot line.
Justified by Tali in Mass Effect. Her species has spent the last 300 years on completely sterile ships, so their immune systems are practically nonexistant. Anyone leaving the fleet is forced to wear full-body armored environment suits, otherwise they'll die of airborne infection in days. In the second game, a male Shepard can romance Tali. During the love scene, Shepard removes the mask, and gets a good look at her face. However, the scene is shot from behind Tali, so the player does not see her face.
When the camera is focuses on her helmet, you can see her eyes and vague facial features- her face looks (at least superficially) similar to a human's.
Tali lampshades this after playing poker with Shepard and members of the engineering crew: "And I thought I had a good poker face."
The third game ultimately revealed quarians to be facially Rubber-Forehead Aliens whose most inhuman facial features were the glowing yellow eyes and a few unusual skin patterns. This was shown not by taking off Tali's mask on camera and leaving the camera on her, but by having her leave a photograph in Shepard's cabin upon saving the quarians during the Rannoch arc, which was a photoshop of a stock image, and in the Extended Cut, a brief slideshow picture of a maskless quarian assuming you brought about geth/quarian peace and chose the Synthesis ending.
In addition to quarians, the Mass Effect universe also gives us the volus, a race of beings from a very-high-pressure world with an ammonia atmosphere. In addition to not being able to breath without a mask, they would explode without a suit.
In the third game's multiplayer, a few of the multiplayer characters wear helmets. What is notable is that every single human wears a helmet. Probably because while it's acceptable for a few dozen aliens to all look pretty much identical...
Vanitas from Kingdom Hearts: Birth By Sleep transcends the normal way of remaining ambiguous in the series by wearing a mask-helmet-thing to hide his face, so he can pull off all of his badass stunts without restraint. He's seen with the helmet removed at least once (before The Reveal, anyway); however, his face is hidden by the camera angle.
Kingdom Hearts has this as a requirement for every game, the first one ends with us just about to see a spiky-haired blonde "Roxas" before the camera stops, and the same in Sora's story in Kingdom Hearts: Chain of Memories. In Riku's story we finally see him... but now part of Riku's face is hidden to hide his blindfold. In Kingdom Hearts II not only do the Organization cloaks hide most Nobody's faces, but the Masked Boy in the extra scene, and (in Final Mix) the Lingering Sentiment, who are revealed in Birth By Sleep, only for Young Master Xehanort to be hidden. In Kingdom Hearts 3D [Dream Drop Distance], 6 members of the new Organization XIII hide their faces beneath the usual dark cloaks, but Young Master Xehanort's face is clearly seen this time, including in the secret ending.
The Pyro from Team Fortress 2, to the point where even the gender is ambiguous. In fact, we're not even sure that the Pyro is a human being. Or any organic lifeform, for that matter.
The Zettai Ryouiki NEW android app from Hastysoft stars a busty redheaded girl whose eyes are never shown - even in angles that would, she does the developers the favour of covering them with her hands!
Carmine from Gears of War is a (different) named soldier present in each installment who always wears his helmet while every other named soldier doesn't.
The Shy Guys from the Super Mario Bros. series. They all wear masks, and the trope is played straight even through Mario Power Tennis, where the Shy Guy's mask comes off during a cutscene. Luigi is the only one who sees its face, and all we get is his Reaction Shot. This is also played straight in Luigi's Mansion where, AGAIN, Luigi is the only one who sees them sans masks... but all you see is two yellow eyes in a dark void, meaning that they still count, specially since it's implied that they aren't "real" ghosts, but creations of Vincent Van Gore.
The player characters in Spiral Knights have their faces hidden in shadow with only their eyes peering out. This is to make them look gender neutral, as the only way to make your character look like a female is to wear a feminine-looking armor set or accessories, and also to keep the player in the dark about their race.
All of the wizards in Magicka, including NPCs and the Big Bad, have their faces permanently hidden in the darkness of their hoods, with the exception of Vlad (who is not a vampire). In fact, every set of robes you can get for your wizards has the same hood, resulting in the same face-hiding. Strangely, they're all still surprisingly expressive.
The Mortal Kombat series has a few examples, most notably the various ninjas, though a couple of them have appeared unmasked, and Kabal. In Kabal's case, it's because his face was scarred in an attack by Shao Kahn's death squads that requires him to constantly wear a mask that doubles as a respirator. One of his fatalities does involve him removing the mask, causing his opponent to literally die of fright upon seeing his uncovered face. A pre-scarring Kabal appeared without a mask in Shaolin Monks, but it doesn't really count since that game is not canon to the main series. He has a slightly different face in Mortal Kombat 9. The new canonical story mode reveals that he has pale, almost grayish skin and dark hair with piercing light green eyes. This all naturally goes out the window when he is once again nearly burned to death, reverting him to the familiar scarred, burned complexion.
A few of the characters from Killing Floor wear gas masks, or otherwise face-obscuring fashion, the aforementioned Pyro even being one (technically two) of them. The most famous of these, however, is without a doubt the ever popular Mr. Foster◊, whose gas mask was apparently impressive enough that the Pyro decided to get one just like it◊.
Shadar from Ni No Kuni is not unlike the page image, right up to his final moments.
Professor Granz Florian of Magical Girl Lyrical Nanoha A's Portable: The Gears of Destiny was only shown once at the beginning, which shows him with his two daughters when they were kids. One of said daughters was happily waving her arms around, coincidentally covering his face with the stuffed toy she was carrying.
In Fallout: New Vegas, Legate Lanius, The Dragon to Caesar, wears a concealing mask almost all the time. He supposedly only takes it off in the privacy of his own quarters, where he's attended by slaves that he's blinded specifically so that they can't see his face. You can't even take the mask off of him when you kill him, because he's the last opponent, and the game turns into a cutscene followed by the end after that.