Batman. Even villains who think Superman's a chump fear Batman. Any other hero inspires caution in criminals, Batman inspires superstitious, pants-crapping horror. He's so horrifying, the Sinestro Corps actually tried to recruit him.
And in the Flashpoint arc, we find out that our Batman (Bruce Wayne) is sunshine and rainbows compared to the one in the timeline where Bruce was killed in Crime Alley and Thomas Wayne became Batman.
The Batman in Batman: Year 100 uses this heavily in his war against corrupt federal agents, going so far as to bring prosthetic vampire teeth on missions to encourage his image as an otherworldly demon.
However, one criminal in Batman The Black Mirror recounted he moved back to Gotham because when he tried to commit a crime in Metropolis, he suddenly found himself 10,000 feet in the air with a friendly voice saying "Don't you think you should change your life?".
Sometimes the Huntress is depicted this way, to an even greater extent than Batman: In Huntress/Spoiler: Blunt Trauma, the Cluemaster tells his daughter that Huntress is "not like that overgrown ferret and his brat. She's gonna kill your old man if she gets the chance." At other times, Huntress is shown to be less feared by Gotham's criminals than is Batman, even though she is much more likely to kill them.
The Joker - just mentioning him to any superhero and villain in the DCU other than Batman (even to some of the most powerful villains and heroes in the DCU) instantly kills a conversation, and even supervillains keep a healthy distance from him. As The Trickster said: "When super-villains want to scare each other, they tell Joker stories."
Bane isn’t called that for nothing. He earned his name by murdering another inmate at a young age while growing up within a harsh prison, and he only became more fearsome after that. During Knightfall, Batman himself was afraid of Bane, because he knew Bane had put him at a great disadvantage and was indirectly causing more chaos than any other enemy before. Ever since that incident Batman has known not to take Bane lightly. And by “breaking” the Batman, Bane earned such a reputation that at least most street levelers of DCU are intimidated by him.
Batman villain Killer Croc, to just about any non-super who isn't Batman, and even he's cautious when dealing with him. Croc switches between Chaotic/Neutral Evil or Chaotic Neutral depending on the writer, but God help the idiots who manage to piss him off and aren't as prepared as the Bat to deal with him.
Amanda Waller in just about every incarnation of her. That is very remarkable for a woman who, either slender or large, is always depicted as having absolutely no powers or master martial prowess whatsoever, and even the fact that she's the leader of A.R.G.U.S shouldn't say much, as there're incompetent government officials aplenty in the DC Universe. What makes Waller so terrifying is just how ruthless she is when it comes to getting things done. She captures villains, implants bombs in their necks and forces them to work for her Suicide Squad, and has no qualms about blowing them up if she has to. Not only that, but she works against heroes almost as much as she goes against villains, simply because the heroes are mostly out of her control. To put it simply, Cracked described her as "the kind of superspy who emerges from the shadows behind Batman to tell him when he's being a dick."
Iron Man is now this to the Dark Elves of Svartalfheim, who are basically The Fair Folk on crack, with even Malekith the Accursed, an incredibly powerful psychopathic sorcerer who fights and actively trollsThor, being wary of him at the very least. Malekith also comments, after Tony, in a Cold Iron armour, tears his way through Svartalfheim hunting for the rings of the Mandarin (which Malekith had acquiring by murdering the former owners), that the upshot of it is that they now have a new story to terrify the children with.
Rorschach from Watchmen, even more so than Dr. Manhattan. During the riots people argued with Doc, but the rioters cleared by Rorschach simply walked away once he made his appearance.
Darkseid. There are very few people in The DCU who can face him alone, knowing what he is capable of doing, without showing a hint of fear. If he wasn't one of these before Final Crisis, he probably is now. Put it this way for those of you unfamiliar - he's the Anthropomorphic Personification of the Platonic Ideal of Tyranny. And has the power and influence to match.
Shown brilliantly in the penultimate episode of Justice League Unlimited when the rest of the villains try to resurrect Brainiac but accidentally resurrect Darkseid. The Oh Crap! faces they all make speak volumes.
How bad is he? He's so bad that Batman himself is willing to break the "one rule" to put an end to his reign.
The New 52 had Darkseid's first appearance showing him getting his ass kicked by the Justice League in their first team up, which led to fears of Villain Decay...until his personal comic came out during villain's month, and it was revealed that after his first defeat, he systematically invaded other versions of Earth specifically to hunt down and destroy the Justice Leagues of those worlds. At the end of the comic, there's an entire room full of Superman corpses.
On a more humorous note, the tiny alien dragon Lockheed is this for the Brood.
Venom, the Evil Counterpart to Spider-Man, was widely feared in the supervillain community in his heyday. Which makes sense when you think about it: If Spidey's foes get beaten by Spidey all the time, imagine how they would feel about a stronger and deadlier version of Spider-Man who is perfectly willing to kill.
The symbiotes have this reputation throughout the galaxy, as Flash Thompson learns when he joins the Guardians of the Galaxy.
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.
At one point in the MAX series, a hardened mercenary from the Balkans drops to his knees and starts sobbing and praying at the mere sight of the white skull.
This goes as far back as the his first comic, Circle of Blood, where at the start Frank is incarcerated in Riker's Island for the third time, and most of its population are afraid for their lives.
Sabretooth is a sadistic, completely unhinged psychopath who treats everyone not allied with him as prey to be hunted down and slaughtered. This would be enough to make a lot of people nervous, but the worst part is that the bastard is smart. Not only is he a centuries-old professional soldier/mercenary who has been trained by countless agencies and fought in innumerable wars, but he's an exceptionally adept manipulator who can play almost anyone like a puppet without their even knowing. Just mentioning his name or the fact that you hired him is enough to cause alarm in a good portion of the MU.
Wolverine got similar treatment in one storyline when the Hand resurrected and brainwashed him into being an agent of HYDRA. This makes perfect sense, since evil Wolverine essentially is Sabretooth.
Fantastic Four. There is barely a single supervillain out there who hasn't at the very least heard horror stories about their terrifying badassery and feats of awesome. Like the Doctor below, they have entire races of aliens, most of whom they don't even remember meeting, who tell tales about them as mythical bogeymen to scare their children with. Case in point:
Reed: It turns out they speak trinary code. So I said to them, "I am Reed Richards of the Fantastic Four, and I..."
Sue: Go on...
Reed: Actually, that's as far as I got. It was enough to send them running.
Even among people who've never actually met the Four, the prospect of facing people who defeatedGalactus (more than once!) would legitimately be terrifying.
The team has developed a mythic reputation on some planets who have tried to invade Earth, only to be challenged by them and have their asses kicked; the cultures of these planets think of them in the same way Earth thinks of The Four Horsemen of the Apocalypse.
In the Ultimate Universe, Reed Richards goes through a Face–Heel Turn and effectively becomes Ultimate Doctor Doom complete with facial scarring. The storyline covering this is titled "Ultimate Enemy" for good reason.
Always a Bigger Fish; the demonic living superweapon Zom scares the hell out of Dormammu's sister, Umar (who's roughly his equal in power), and took the combined efforts of Dormammu and Eternity (along with unnamed others) to seal in a can. Imagine how Dormammu must feel about Zom if he was willing to work with Eternity to stop it.
Bizarrely enough, Shuma Gorath is a lesser example of this compared to Dormammu and Zom despite being a Lovecraftian horror more powerful than Dormammu and on par with Zom (if not stronger). This is due to Shuma Gorath's Charm Person powers that make everyone it rules over revere it. Everyone not under its influence and aware of its existence fears it.
The DC Universe has the Anti-Monitor. Only rarely seen as an actual Big Bad, he's referred to often as a greater threat than whoever is at the moment. How bad is he? Well, after defeating Death itself in Blackest Night, Ganthet tells the Green Lantern that they've actually lost because the Anti-Monitor has been freed.
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 leave... 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."
Galactus, the devourer of worlds, counts for self-explaining reasons, though he can be reasoned with. Unlike his counterpart from Earth-1610, who kills organic life just because it is disgusted by it... and then 616 Galactus ended up in the Ultimate Universe and promptly made that version of Galactus his new Herald.
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 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 the Fan Disservice. Many of them are fairly certain he's insane even by cape standards.
One of the requirements to be part of the Sinestro Corps is that you need the ability to inspire great fear (it's their specialty in the emotional spectrum). They aren't kidding. Their ranks include a hulking drill instructor who happily eats those who fail, an emotionally numb crustacean who can snipe from three space sectors away, an alien who kills parents and takes their children, and an insectoid Eldritch AbominationEnergy Being who possessed the Green Lantern's greatest hero. And again, a Sinestro Corps Ring tried to recruit Batman; they settled for the Scarecrow (himself quite a worthy candidate) during Blackest Night.
The Incredible Hulk scares the hell out of the rest of the Marvel Universe. The most powerful heroes - even knowing full well he's not evil, just misunderstood - take his arrival as seriously as that of someone like Doctor Doom, if not more. Given what a rampaging Hulk can do, it's not without reason. He could get angry, you see. And you wouldn't like him when he's angry.
In recent stories, people are starting to wonder if Banner is actually the more dangerous one. He is.
Deadpool had a memorable meltdown when he found out that he had to get a blood sample from the big green galoot in an attempt to cure his currently-failing Healing Factor. His reaction was to talk him up using the lyrics of his old cartoon theme song ("Ain't he unglamorous").
Subverted with Captain America. He not only holds immense respect for him in either form (he bitched out the Illuminati for sending Hulk into space) but it has been said by numerous characters that the only thing Cap would need to do to stop a rampaging Hulk would be to stand in front of him.
Junior from Secret Six manages to run most of the crime on the west coast because all the other criminals and supervillains in The DCU, even the ones from Gotham, like The Joker, are terrified of Junior.
Also, Paperinik himself. 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, even for Trauma, an Evron super-soldier with the psychic ability of creating fear with his mere presence (Paperinik actually felt the fear, he just took the adrenaline rush that came with it to continue fighting, scaring Trauma into submission). Best shown in issue 37: 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.
A non-PKNA 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.
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).
A humorous example is Ariella Kent, an alternate universe daughter of Superman and Supergirl (Linda Danvers). She's a mere 6-year-old girl who obliviously causes chaos and destruction wherever she goes. Several alien civilizations call her R'E'L, the Destroyer of Worlds.
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.
Nobody likes Red Skull. Nobody. Dropping his name in casual conversation in the Marvel universe underworld will cause everyone to go quiet and stare at you. Doctor Doom and Magneto have both tried to kill him... not because he got in their way, but just to get rid of him.note Though Doctor Doom is Roma and Magneto is Jewish, so they've got a damn good reason to hate Red Skull When he briefly disappeared (thanks to Magneto's attempt on his life), his return caused Captain America to have a temporary Heroic B.S.O.D..
Notably, in a rare DC/Marvel crossover story the Red Skull teamed up with the Joker to enact a villainous scheme. Their alliance lasted up until the point when the Joker was informed that the Red Skull was, in fact, a real Nazi, and he wasn't just wearing a swastika for kicks. At that point the Joker pulled a gun and officially dissolved their partnership. That's right, kids. Even the Joker refuses to associate with the Red Skull.
Thanos the Mad Titan is a name/title that not only gains attention from every last hero on Earth when dropped, but also from the likes of Galactus. He is completely unpredictable, and every time he is scheming on another plan, you can be sure a catastrophe is about to follow.
The Sentinels are this to the whole Mutant society, especially after the Genosha-Massacre. They are the ultimate embodiment of senseless racism and cruel genocide in the Marvel Universe. This causes problems for Juston, in-universe and out, since his Robot Buddy is a Sentinel.
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.
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.
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 away fot 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.
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.
In Atomic Robo, everyone is afraid of Jenkins except Robo. When two of his coworkers accidentally kill his orchid in "Once Upon A Time In Mexico", they flee the country.
Diabolik is called King of Terror. Given his body count, it's more an affectionate nickname than anything.
Squirrel Girl has gotten this reputation among many supervillains and organizations, to the point where they refer to her as "The Anti-Life" and "The Slayer of all that Breathes"