One Girl Guy Army A villain character named Vonbastion doesn't show a face, or mouth behind the cloak. A very calm and unknowing character. Doesn't even show it's Gender to anyone including the reader.
Sam and Fuzzy has numerous characters which fall under the masked variety. Though they are primarily mooks or secondary characters (and ALWAYS ninjas), Mr. Blank and Mr. Black served as major characters for one story arc. They were also distinguished by having their masks fully conceal their faces. Most other ninjas have an opening for the eyes, but their eyes are only drawn rarely. Mr. X and Mr. Y are also recurring characters who often cover their entire face, but sometimes reveal their mouths.
The Adventures of Dr. McNinja has a Cerebus Retcon involving how none of the McNinjas ever take off their masks, even to eat or vomit. As nobody has seen their faces, they can remove the mask to disguise their identity and vanish.
Clifford Mayers, the main villain and scheming billionaire in Funny Farm has an unexplained shadow covering the upper half of his face apparently caused by his characteristic hair, regardless of where the light is coming from. The shadow disappears later in the story when his evil plans are foiled, and begins to reappear as he gets back into the scheming. Flashbacks from before he turned evil also reveals him as shadow-less.
When he wore dark glasses as part of a disguise, he sometimes displayed Scary Shiny Glasses instead (even though you couldn't see his eyes anyway...)
Cartoonist Bill Hollbrook gets big mileage out of this trope:
In Kevin & Kell, Kell's boss, R.L., is only shown as a protruding - usually salivating - wolf snout (And occasionally his arms).
In Safe Havens, Don, one of Dave's teammates is always shown with his head out-of-panel. The now-retired character Miss Callowood also never showed her face. Rosalind, one of Samantha's lab assistants, was portrayed similarly to Don, until a lab accident caused her to shrink a foot. She didn't mind a bit as her height made her extremely self-concious.
Othar Tryggvassen (Gentleman Adventurer!!), from his very first appearance in Girl Genius, wears a spiffy silver visor over his eyes. Astonishingly, when his eyes are shown, they're the prettiest shade of baby blue imaginable.
Lampshaded in The Wotch. Up until recently, Xaos/the Worlock had always been seen with a helmet that hid the upper half of his face, if not all of it. In this comic, we finally see him without his helmet on (in a flashback), and in the first two panels in which he appears, the upper half of his face is obscured by a tree branch. He then moves it out of the way, muttering, "Stupid tree branch keeps getting in my face".
I still have no explanation for Miss Conrad's head.
In Sluggy Freelance, HeretiCorp's board room is specifically designed to keep everyone's faces hidden in shadows. Since many of these characters are rarely seen outside the board room (including Diabolical Mastermind Daedalus), it takes quite a while before readers get a good look at their faces. Daedalus in particular gets very annoyed if someone turns on the lights inside the board room and will usually cover his face until they're turned off again.
An active parody of this in Looking for Group: Richard's features are never shown clearly. Only his eyes are visible and the rest of his face is covered by a veil at all times. The character is inherently evil, so it's more than likely a parody.
In the Mr. & Mrs. Rockhound cartoons of The KA Mics Mr. Rockhound's cousin Lenny is usually off-screen, but on the few occasions that he's 'appeared' the lights were out & we just saw his eyes, another time he wore a penguin costume so we just saw his eyes & tail, another time a rock had fallen on him so we just saw his hand.
In Life And Death Steve was like this originally, because he didn't want anyone to see his scarred face, but he's gotten that fixed. Bobby's face is, so far, kept secret from the audience, but Brunhilda thought it was very good looking.
In Harkovast, the Wizard Quinn-Tain is only seen from behind.
Decoy Octopus from The Last Days of Foxhound typically takes on the appearance of one of his coworkers. However, when he appears in a spiritual realm, such as when he is tested by The Sorrow, he appears as only a fedora and a trenchcoat, with no face or body.
In Dominic Deegan, in his first few appearances, the King of Callan's face was either just off panel, or in one case behind a voice bubble. He's eventually revealed to have a perfectly normal face, save his Monochromatic Eyes.
In Mutant Ninja Turtles Gaiden, after 17 chapters, we had never seen Augustus Amherst's original, pre-Renoir, face. Even in flashbacks he's NEVER seen.
In Blip, The Adversary has several layers of this. In his first appearance, in one of K's lucid dreams, K wills herself awake before he can appear on-panel. When he finally shows up on-panel, his face is obscured via in-story pixellation. Then the pixellation is removed, and he's wearing a white mask underneath it.
Anthony Carver in Gunnerkrigg Court, at least as an adult. Fitting, considering that (as of Ch 27) we know less of him and his motivation than any other major character in the comic.
In Voldemorts Children, both Voldemort and Dumbledore usually appear with the top halves of their heads concealed in shadow, so that only a mouth is visible.
The bounty hunter Maricax in Jix is always shown wearing a mask, except for one time after he had been injured, but his face was wrapped in bandages. All of his other appearances after that showed him wearing a mask.
Batdragon, who is a parody of Batman, in Dragon City always wears his cowl when on screen. This is possibly because none of the main characters of the comic knows what he looks like. There was one instance where he wasn't, but his face was shadowed out for comedic effect.