In the storyline No Man's Land, the person who takes the identity of Batgirl is never shown without her mask until Batman fires her, at which point she's revealed to be Huntress.
In Death of the Family, The Joker's...face has not been shown. He has taken back his face-skin and is wearing it as a creepy mask. It's safe to say that his face is not a pretty sight.
The Robin villain Jaeger goes through a few hi-tech face covering masks but by the time he's in police custody and they go to remove the one he's currently wearing it has been surgically grafted to his face so his face is never shown.
The villain Mano wore a transparent bubble helmet filled with the poisonous gases he needed to breathe so all the reader ever saw was a shadowy silhouette of his head.
Another villain example is the Time Trapper (in every of his many identities). His face is always in shadow from the hood of his tattered purple robe.
Ferro Lad is basically a heroic Dr Doom with transformation powers.
In Superman comics, Tiny Bubbles, a superstrong Intergang enforcer had her face constantly obscured (from the reader, but not from other characters). When a reader wrote to the editor to ask about this, they said it just seemed like a fun idea.
Rorschach from Watchmen keeps his face hidden behind a shifting black-and-white mask, though he argues that that is his real face. He's not shy about taking it off during the day to walk around, spy on people in plain sight, and predict the end of the world.
Doctor Doom, enemy of the Fantastic Four, another deformed-beneath-the-mask type. Doom may be one of the longest-running examples of this trope; Marvel has enforced an ironclad "Doom's face is never shown!" rule for over fifty years. Characters who do see his face are almost invariably filled with a mix of extreme disgust and abject terror.
Doom's face before the accident that deformed him is sometimes shown in Flashbacks. There's also Secret Wars, where his face is (temporarily) fixed.
Mary Jane Watson was The Ghost until The Amazing Spider-Man #42, though on one occasion prior to that, she appeared with her face obscured by a potted plant.
This also had the effect that, since we never saw her face, and Peter was continually avoiding being set up with her on the assumption she wasn't attractive, the readers had the same surprise as him when he answered the door to her in a Splash Panel.
The Green Goblin, in his first appearances, was always either wearing his mask or had his face obscured by some random object.
Taskmaster does better than most costumed types at concealing his true name and face; he never takes off his mask in-panel, whether others are around or not. When he is defeated and his mask is stolen in his own miniseries, we see him only in silhouette, and then from behind, before he retrieves his mask and makes sure the ones who took it aren't going to be telling anyone.
One of the Udon comics actually did show him without the mask on... in a flashback to when he was twelve or so.
Goes so far that when he's working with Deadpool and wearing a copy of his costume, he can be seen wearing his traditional skull mask underneath his Deadpool mask.
It was shown once when Moon Knight defeated him and threatened to cut off his face literally but instead decided to just cut his mask off.
Both incarnations of the Captain America's villain Baron Zemo have had their masks literally fused to their face. The younger Baron eventually finds a way to remove his, but his face is horribly scarred underneath.
The Punisher MAX - Subverted and averted with Finn Cooley. An Irish bomb-maker, his face was blown off, so he was grotesque and disfigured, and his face was shown frequently during the "Kitchen Irish" storyline.
Guardians of the Galaxy: In Vol 2. the Badoon refuse to show their faces to anyone, because despite being hideously ugly lizard-folk, they think they're beautiful, and that no-one else is fit to look at them.
Simon Bisley did once draw his version of a helmetless Dredd, but the picture was covered up in the final comic. Gaze into the face of Dredd◊.
Subverted with Judge Death. At first, he is built up as an Evil Counterpart to Dredd complete with a warped version of his Iconic Outfit. In his Origin Story, he is shown as a human being sans helmet and how he became an undead monster.
Judge Fear: we never see his true face, just his helmet, which covers all his face and which he can open, which is apparently so frightening it can scare people to death — gaze into the face of fear! Does not always work: Dredd: gaze into the fist of Dredd! Fear is a bit of an odd case in that he literally doesn't have a face of any sort, it's always just a psychic projection.
In American Born Chinese, Jin and Danny's parents always have their faces partially or completely hidden. Subverted when Danny's parents are finally shown, revealing that Danny's parents are Jin's parents (since Danny and Jin are the same person).
Brave Chef Brianna: When Sven Jakobsson reunites his children to tell them how he'll decide which one will take over his cooking empire, the readers cannot see his face because a chandelier is blocking it from view. In a latter issue, a speech baloon covers his face.
Chick Tracts often portray God as an enormous throned figure whose face is silhouetted by light, making him look eerily like The Blank.
Lampshaded in the Cracked parody of The Fall Guy. Colt asks Big Jack why she is suddenly wearing elaborate hats that conceal her face. Big Jack replies that the artist couldn't get her face right so decided to hide it behind the hat.
The Phantom Blot from Mickey Mouse Comic Universe. In Mickey Mouse Outwits The Phantom Blot by Floyd Gottfredson, Mickey Mouse meets the Phantom Blot for the first time and, well, outwits him, so he is unmasked at the end, showing him to have a striking resemblance to Walt Disney. However, later appearances in American Disney comics (often drawn by Paul Murry) never showed The Blot's face. He would sometimes wear masks that looked exactly like a human face on top of his black hood... but we are even told on-panel in one comic that no one has ever seen his face (which is weird, since he regularly ends in jail - shouldn't they remove his hood then?). In European Disney comics, however, the unmasking was canon, and he regularly appeared without his hood - after all, it made him less conspicuous to the public.
It gets weirder: Egmont, the standard Disney publisher in northern europe, decided to make both, the unmasked Phantom and the never unmasked one, separate characters, often changing details when translating italian comics to do so. The unmasked version is named "Plattnase" (Flatnose) and often doesn't were the hood in the whole story while the masked version is called "Schwarzes Phantom" (Black Phantom)and Mickey sometimes doubts that he is even human (well, the local equivalent of human). Recently, they have become the same character again, though.
From Dork Tower: Leslie, Bill's (sole) employee at Pegasaurus Games, is always shown with her face half-hidden behind the store counter.
Flaming Carrot - Carrot's identity is kept a mystery to the reader, and the only time we see him without his mask is when his face is covered in bandages. According to some theories, he's actually Jim Morrison.
In Gaston Lagaffe, the main character's boss Mr. Dupuis is never shown, presumably because he is a real person.
The Surgeon General from Give Me Liberty, whose face is always obscured by a surgical mask, cap, and tinted goggles.
In Le Scorpion, Captain Rochnan's face is not revealed until The Treasure of the Templars; his face being concealed by his armoured helmet before this. And he falls to death not long after the reveal.
In Paperinik New Adventures Camera 9's face (except for his beak) is always covered by his camera or (when it takes it off) by Scenery Censor. This was to enforce his belief that his job as cameraman (he was a very famous photographer once) transformed him in a mindless robot, since he thinks television is a shallow and loud way to reports news.
When Korinna was using the fake identity "Profunda", her face was always covered until The Reveal.
This is one of the trademarks of The Phantom (Ghost Who Walks, Man Who Cannot Die, etc.). When in costume he has his mask, and when travelling incognito as "Mr. Walker" he wears a hat and sunglasses all the time, claiming that he has a disfiguring skin condition when asked to remove them. If he isn't wearing the mask or the hat and glasses for some reason, he's either drawn from the back or in shadow to obscure his face.
Preacher - John Wayne acted as a spirit guide to Jesse Custer. His face was always in shadow, even in the middle of Monument Valley with no shade. A similar thing occurs with the mysterious fat guy that Jesse gives a lift to in issue #53.
Subverted in Radioactive Man by one of the members of "The Bonfire Club", sitting in shadow an profile, one of whom is clearly Richard Nixon:
"Gee, it sure is dark in here. You'd think with all our power and money we could afford a few lightbulbs."
Arch-villain The Octopus in The Spirit is only ever seen as a hand or pair of hands wearing distinctive gloves.
In Swordquest, the mysterious oracles Mentorr and Mentarra wear hooded robes that leave their faces entirely in shadow.
Monsieur Choc, the arch-villain in Tif et Tondu is never seen without a knight's helmet that completely disguises his features. In the two page comic L'Image de Choc one character eventually get hold of a picture of Choc without his helmet. However, the picture turns out to be useless Since it depicts Choc when he was an infant.
Variation: Usagi Yojimbo's Big Bad, Lord Hijiki, is one of these—but only after his face is completely shown in his first appearance.
V in V for Vendetta chooses to remain behind his mask for the entire duration of the narrative, save for his revealing himself to Dr. Delia Surridge as she lays dying. She comments that his hideously burn-scarred face is "so beautiful..." This trope exists partly because V is more embodied as an idea than as an individual.
An X-Files comic about the Fatima Prophecies had a scene with the Pope and a military commander discussing the third (unopened) prophecy. There were no backgrounds or faces, just the two symbolic outfits of "military" and "church".
In Zot!, the electronic assassin 9-Jack-9 has no face. (Creating difficulty for creator Scott McCloud when he held a contest for which character the readers most wanted to see hit in the face with a pie, and 9-Jack-9 won. It ended up passing through him and hitting Zot, the runner-up, instead.)