In some stories in both DC and Marvel universes, humanity (and/or Earth) itself. In the Marvel Universe various alien races are simply flat out-terrified by the sole planet that has not only forced Galactus to bail out... multiple times, but has beaten off invasions by galaxy-spanning empires. In one notable case, when this information was brought to the attention of a soon-to-be-invading fleet's commander, the fleet immediately turned and got out of the area as fast as they could. At the end of the Ultimate Galactus Trilogy by Warren Ellis, Nick Fury sends Vision out into space not only with directions on how to defeat Galactus, but also with a little message from Earth: "Human beings can kick the hell out of anything."
In Atomic Robo, everyone is afraid of Jenkins except Robo, and that exception is mostly because Robo trusts him, not because he thinks he'd actually stand a chance if the two actually fought. When two of his coworkers accidentally kill his orchid in "Once Upon A Time In Mexico", they flee the country. A government conspiracy drops an entire squad in nine foot suits of Powered Armor on him and even they learn to fear him. After Jenkins becomes a Zombie Infectee during an attack from the Vampire Dimension and ALAN has to Mercy Kill him, Robo tells ALAN that he probably saved everyone in that room - Robo included - and possibly everyone in the world from the kind of damage a vampire Jenkins could do.
Button Man: Harry survives so many Games at such incredible odds that he eventually becomes feared as a walking incarnation of death, to the point that even the Voices are terrified of him.
Hugin, aka "The Raven", is by far and away the most feared member of the Death Vigil. He demonstrates why in the first issue, when he turns into an allosaurus and one-shots an Eldritch Abomination that was throwing protagonist Sam around like a rag doll moments before.
Diabolik is called King of Terror. Given his body count, it's more an affectionate nickname than anything. The strange part is how it started: it was eventually revealed that when he came to Clerville Diabolik wanted to keep a low profile and said just that to his lover at the time, Natasha Morgan, who was instead encouraging to use the few rumors that had started to be this once she retired... And then one day an airplane launched an SOS announcing that Diabolik was about to crash it before being effectively crashed and sunk, with not even Diabolik knowing what had happened until the plane was recovered and Natasha's body was found inside (some of Diabolik's old enemies had kidnapped her to use her as hostage, and rather than letting them she killed her way to the cockpit, forced the pilot to make the announcement, and then crashed the plane).
Diabolik takes advantage of the terror he causes, and whenever someone tries to threaten his status as the King of Terror he immediately moves to prove he's just that fearsome. A newspaper's star journalist was calling him a two-bits crook and the police incompetent for failing to stop him, and Diabolik made said journalist drop dead in the middle of a speech he was giving to insult Diabolik and the police even furthernote Diabolik, knowing he had the habit of licking his finger before turning a page, soaked his speech's script in cyanide. The journalist unknowingly assumed a bit of cyanide every time he turned a page of the script until he died and then did the same to the paper's director in the middle of lunch apparently by just telling him he'd die in seven days.note Diabolik had drugged and kidnapped him as part of the hit on the journalist, and as he was there put a cyanide capsule in one of his teeth and, knowing he tended to grind his teeth every time he was nervous, told him he'd drop dead in seven days to make sure he'd do just that and eventually break the capsule A convention of criminologists called him incompetent and declared that a brave cop could easily stop him, causing Ginko, the cop assigned to try and stop him and the one to actually making him fail from time to time, to resign from the police in protest, and Diabolik proceeded to troll the police and make a mockery of Ginko's replacement until the criminologists ate their words and the replacement quit in disgrace (the fact he used the trolling to set up a heist that Ginko and a few cops loyal to him managed to foil helped). A show at a luna park depicted Diabolik as unable to kill an unarmored person on the spot by throwing his knife (the only time that happened, Diabolik had thrown a paper knife), and Diabolik stole his wife's jewels.
Paperinik. He may be just the superhero persona of Donald Duck, but he's quite smart (no supergenius but still smart), has no qualms about hurting or even killing you in the most humiliating fashion, knows how to knock out foes much bigger than him, and is just impossible to scare, not even if you have the psychic ability of creating fear with your mere presence (Paperinik actually felt the fear, he just took the adrenaline rush that came with it to continue fighting, scaring his opponent into submission).
A story starts with the criminals of Duckburg describing him as six floors tall, seeing everything with his hundred eyes, armed with invincible superweapons, having at least four hands ("I was too busy to count them!"), and generally being invincible, and ends with the criminals (including one from out of town that was skeptical about Paperinik's myth) saying he's twelve floors tall, with a thousand eyes and invincible weapons, and, worst of all, scarily cunning - after he apparently threw a few fight to lure them all in the same place and capture every single criminal in Duckburg (his equipment was malfunctioning, and after fixing it he claimed it was all according to plan to preserve his reputation). Other stories show that most of Duckburg's criminals have developed a Friendly Enemies relationship with him because they know they can't escape or beat him but if they surrender he won't give them a horrific beatdown.
In issue 37 of Paperinik New Adventures an Evron soldier who had a tour of duty on Earth was utterly terrified and unable to do anything but babble in terror when he encountered Paperinik on the Imperial Worldship. Evronians are emotionally stunted.
Xadhoom, a Xerbian who has mutated into a Physical Goddess to try and solve her people's impending energy lack problems only to discover that during her experiment the Evrons had used a clause of the commercial treaty she had stipulated with them to invade and destroy the Xerbians. Since then Xadhoom has a vendetta against them, and they're utterly terrified of her: she's positively invulnerable, and can fire blasts of any form of energy with the power to fry a single Evron, annihilate one of their battlecruisers, and anything in between. Also, Xadhoom means "Creditor" in Xerbian, as the Evronians owe her her whole world.
Trauma, the Evron super-soldier. Once just Evron's best and most aggressive general, he voluntereed for a super-soldier experiment, becoming the size of a small mecha, incredibly strong, Immune to Bullets (he has been shot on screen for no effect), and gifted with the psychic ability to cause immense fear and absorbing it, transforming his victims into coolflames (the emotionless slaves of Evron).
Pete is well feared among Mouseton's criminals for a very good reason: if you doublecross him he will beat the crap out of you and rob you blind or get arrested trying, and doesn't care if he gets arrested as long as he drags you to jail with him. Even Phantom Blot doesn't dare to doublecross him, and whenever they work together he offers him a good deal and keeps his word.
Deathmonger, a necromancer who has killed countless superheroes and turned them into undead minions. Many superheroes avoid Deathmonger out of fear of adding to her ranks.
The only reason Willy Pete isn't this is because he likes to keep a low profile. Though after singlehandedly wiping out an entire team of superheroes, that's likely to change.
And on the other side of the coin, villains react this way to Maidman, who's essentially Batman in drag, except more brutal — and scarier due to the Fan Disservice. Many of them are fairly certain he's insane even by cape standards.
In Gold Digger, Dreadwing is the most hated villain in the series. He doesn't even have anyone under his command who likes him, as they are all slaves, scheming to usurp him, or are allies who don't trust him at all but have no other choice but to team up with him.
Dreadwing also subverts this trope, as since he's so sadistic he makes enemies out of almost anyone he meets, and it constantly comes back to haunt him at the most inconvenient moments.
The reaper Serpentus is justified by this trope, as while Dreadwing is wretchedly sadistic just for fun, Serpentus has a good reason for making himself hated by everyone: as a reaper his power comes from the hatred in peoples' souls; therefore the more servants and slaves he has under his control that hate him, the more powerful he becomes.
From Hellblazer, John Constantine is one of the only mortals to ever be feared by gods, heaven and hell. In one guest appearance in The Books of Magic, Zatanna and Timothy Hunter unwittingly got themselves cornered and outgunned by a whole army of sorcerers and monsters. When all hope seemed lost, John Constantine suddenly arrived on scene, which got their attention quickly. All he did was light a cigarette, and reminded them what he can do and if they really want to tango with him. At that moment, every hostile suddenly ran for their lives, and Zatanna was confused and impressed. John later explained that since he has a reputation of getting anyone near him killed, nobody ever wants to be near him anymore.
Herbie: Troublemakers of all kinds will panic at the mere sight of Herbie; this includes (but is not limited to) wild animals, witches, monsters, dragons, alien beasts, and angry comets. Herbie's reputation is so widespread that even antagonists from the past and the future are terrified of him — he's not called The Fat Fury for nothing.
Judge Dredd himself. His clone designers specifically named him "Joe Dredd" to instill fear in the populace so they would obey the laws. Dredd is such a renowned and tough-as-nails Judge that perps have been known to surrender in droves the moment they found out who they were dealing with.
While not explicitly mentioned as such nor shown to be one (mainly because most people usually believe him dead), Darkhell from Les Légendaires is strongly hinted to have been a symbol of fear in all Alysia during his time as the ruler of Casthell. His mere presence as the enemy usually is enough to get everyone becoming serious. Considering all the abominations he did, that's strongly justified.
The Sanctuary Tree: The fat female guard. Donald runs away terrified of her when she wants to hit him for fishing in a forbidden lake (and calling her a "whale"), and at the end of the story, when she falls madly in love with him. Even the animals run away in horror as she walks past them after Donald.
Star Trek (IDW): The Klingons regard Tribbles as such dangerous creatures that they transport all of them onto a planet and attempt to blow them up with a timed bomb.
Super Sonic is this in Sonic the Comic. Unlike the heroic Super Mode you can unlock in the games, in this continuity Super Sonic is Sonic's Superpowered Evil Side who comes out to play when Sonic is stressed out enough (or exposed to Chaos energy). Once he's dealt with the immediate threat he'll gladly kill anyone else in the vicinity... even innocents or one of Sonic's friends.
The Bastard from Super Crooks is the most feared supervillain ever, for good reason. He's the kind of guy who will murder a man's whole family and friends, then the man himself, if they wrong him. And of course, Johnny chooses him as his target.
The Transformers: More than Meets the Eye: The Decepticon Justice Division is this to other Decepticons. They hunt down Decepticons that have committed crimes against their faction and horribly murder them. Even Phase-Sixers like Black Shadow aren't safe. Naturally, they're also more than happy to slaughter any Autobots they happen across just as brutally, and the Autobots know it.
The Transformers (IDW): Would you believe that a short, red, heroic robot is this? If not, then you haven't met the violent little ball of fury known as Cliffjumper. An entire Decepticon landing party calls in reinforcements and pull out their biggest guns just because they realize the "little red runt" they're facing is him. It doesn't help them, because Cliffjumper doesn't do 'survivors' when he's good and mad.
The Transformers Megaseries: Thunderwing is a nigh-indestructible Person of Mass Destruction that went on a mindless rampage across Cybertron. The Autobots and Decepticons had to team up to take him down, and despite throwing everything they had at Thunderwing until the planet itself swallowed him up, they know they didn’t actually kill him. Everyone treats the thought of his return with dread, and Optimus Prime has occasional flashbacks to the final battle against him.
The Phase Six Decepticons are this due to their role in the war. They're called in at the end of a campaign to finish off the opposition and cleanse the planet. The fact they don't really distinguish between friend or foe makes them feared by Autobots and Decepticons alike. Overlord takes this even further when he goes AWOL to avoid being limited to this role and sets out committing atrocities to slake his own bloodlust and get Megatron's attention.
Several other Transformers are also defined by how scared people are of them, including pretty much every major Decepticon leader ever shown. Comic book depictions of Straxtus and Galvatron (especially their UK versions) are based in large part around the fear they cause in others.
Most famous outlaws in Lucky Luke to a ridiculous degree, Phil Deffer emptied a whole saloon just by showing up, Billy the Kid asked for the bank's safe while handcuffed and Luke had to threaten the banker to not give it to him and the Daltons get a Ballistic Discount the moment the gun seller recognizes them (one even dropped his weapon when he realized he was pointing it at an unarmed Joe). Luke himself scares most outlaws as the fastest gunman in the West. Played seriously with Black Bart, who not only unnerved the stagecoach that faced natives and bandits a few days ago but he also would have stolen the gold with Luke helpless to stop it if it wasn't for the fact the gold was never there to begin with.
The Texas Rangers are this to the criminals, both because every single one is a formidable badass and because if you succeed in killing the one you're facing every single one will now hunt you down to the end of Earth (Not Hyperbole: the plot of a story was about Tex and Carson chasing the murderer of a Ranger across state lines and not stopping for anything, not even a small Indian rebellion - that they suppressed - while the other Rangers searched and provided useful information).
Carson and especially Tex are much more feared than the rest of the corps, and are routinely described as worse than the plague and cholera put together. Tex is so terrifying that a formidable bandit he once arrested hallucinated him for the rest of his life after two encounters, the one where Tex and his pards wiped out his gang arrested him and one outside the tribunal after he managed to bribe and blackmail judge and jury into acquitting... Assuming the second encounter wasn't the first hallucination.
Mefisto, the closest thing this series has to a Big Bad, is enough to scare pretty much anyone who knows who they're dealing with, to the point that in the last encounter so far Tex, in spite of the many hints, was in denial about him being Back from the Dead because he just didn't want to believe it (that said, once it was clear it was him he managed to defeat him once again). Considering he's an incredibly powerful warlock, whose only limit is that he can't conjure anything solid or hold things through his Astral Projection and depend from his very limited physical strength in combat, and that he managed to get back to life after being devoured alive by rats, it's fully understandable.
Sumalkan, the Black Tiger. And with reasons: he was a Magnificent Bastard planning to literally buy out the US a city at a time and it was actually working, his enemies tend to die no matter what their defenses are, and if his pawns try and betray him he has them clawed to death. That's before you get to the fact he was a Master of Disguise and you could have been talking to him and not realize unless he decided to drop the disguise (as one of his pawns discovered the hard way when he decided to betray him and discussed the plan with the organization's lawyer - actually one of Sumalkan's disguises).
Ishmael of Copperhead is one of the few people able to live outside the town limits because the murderous Natives are too terrified to attack him. When they finally do, he lives up to his reputation.
Doxta of Black Science has such a powerful reputation that the three tribes allied against her debate whether attacking will result in most of them dying or all of them dying.
Vampirella, especially during the Harris years, is often depicted being capable of inspiring both great fear and hatred in the supernatural creatures she hunts and kills as humanity's protector.
Groo the Wanderer has this with the title character: a numbskull barbarian who is so destructively clumsy when he doesn't mean harm, and apocalyptically overwhelming when he does in battle that most people with any sense quake in terror when discovering that he's among them. In fact, there is one story where a village falls into utter chaos and is devastated by the mere rumour that he is approaching, creating a enraged mob ready to attack Groo upon arriving with him genuinely having no way of knowing what has happened.
Scrooge McDuck in The Life and Times of Scrooge McDuck goes through a lot in his life, but he certainly builds up a reputation: From Scottish immigrant to rivercaptain to cowboy to golddigger, by the time he moves to Yukon, most Wild West legends are terrified of him. Even after his years-long retirement, grandpa Beagle passes out in fear when he realizes Scrooge is chasing them.
In the "Hearts of the Yukon" story, there is Superintendent of the Royal Canadian Mounted Police Sam Steele (a real person). Klondike, the most violent, unruly and chaotic town in all the gold rush note Don Rosa is aware that Klondike has been exaggerated over time, but it needded to be chaotic to fit with Scrooge's backstory is emptied entirely when the people there hear that Sam Steele is coming. Scrooge meets an extremely grizzled man using a massive dagger to clean his nails and riding a bear, and he is terrified of Steele.
(a real person). Klondike, the most violent, unruly and chaotic town in all the gold rush note is emptied entirely when the people there hear that Sam Steele is coming. Scrooge meets an extremely grizzled man using a massive dagger to clean his nails and riding a bear, and he is terrified of Steele.