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 Lanterns that they've actually lost because the Anti-Monitor has been freed.
Most villains fear Batman. Any other hero inspires caution in criminals, Batman inspires superstitious, pants-crapping terror. He's so horrifying, the Sinestro Corps actually tried to recruit him - and the Smallville: Season 11 comics took it up a notch.
Yellow Ring: You have the capacity to harvest great - Batman: Take a deeper look. Let it linger. Yellow Ring: *whispers* Harvesting protocols paused. Batman: That's more like it.
And in Flashpoint, 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?"
Batman is so dreaded, Plastic Man was able to help quash a prison riot he, Green Lantern, Aquaman, and Zauriel were trying to deal with in JLA (1997) simply by shapeshifting into a silhouette of Bats.
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. Trickster spells it out in Underworld Unleashed:
Trickster: Great going, Neron, bring in the one guy no one wants to be in the same room with. When super-villains want to scare each other, they tell Joker stories.
On the other side of the spectrum, there are only two people the Joker is deathly scared of: one is The Batman Who Laughs, mentioned later, the other is The Creeper
Bane isn’t called that for nothing. He earned his name by murdering another inmate at a young age while growing up within a Hellhole 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 Batman, Bane earned such a reputation that at least most street levelers of DCU are intimidated by him.
The Scarecrow! Even though Dr. Jonathan Crane may appear to be a hapless dweeb or a schmuck villain, he's just as dangerous a threat to Batman himself. There is a reason why he dubs himself the "MasterofFear", and during Blackest Night, he was recruited by the Sinestro Corps, albeit as theirsecond choice.
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.
Then, there’s the Court Of Owls. What’s most impressive about this one is that they manage to be this despite the fact that 99% of Gotham’s citizens aren’t even aware of their existence. By regular Gotham citizens, they’re usually viewed as a fairy tale meant to frighten children, not unlike how Batman is sometimes viewed by Gotham as an urban legend meant to scare crooks.
Lady Shiva, thanks to her reputation as the World's Best Warrior and an insane Blood Knight. Just mentioning that she's in town is usually enough to scare the shit out of any skilled martial artist. Not even Batman is fond of facing her in a fight.
Mr. Combustible: Oh Oswald... you're scared of a "mob killer"? Really? The Penguin: It's not a mob killer. It's Lady Shiva. Mr. Combustible: Come, girls. Let us find better accommodations for tonight. Girl #1: What? Where? Mr. Combustible: Anywhere but Gotham.
Brainiac is one of the worst enemies of Superman. An incredibly intelligent -and utterly void of empathy and compassion- alien life-form, strong enough to fight Superman with his fists and smart enough to create absolutely unbreakable force fields, Brainiac is infamous for shrinking and stealing whole cities. Suffice it say, Supergirl can bench press a mountain. And in Superman: Brainiac she reveals that she is frightened of Brainiac.
Supergirl: I grew up on Krypton, didn't I? Everyone who did knows about Brainiac. He's what kept us from going out after dark. Superman: You're... scared? Supergirl: It was the scariest thing that ever happened on Krypton. Next to the day it died. I'll never forget Brainiac.
Brainiac originally had the merest touch of humanity, even if it was because he needed to pass himself off as a biological humanoid. In "Brainiac Rebirth", Brainiac rebuilds himself into a nighmarish skele-bot android with incredibly superior knowledge, and any semblance of humanity or feelings removed. After narrowly surviving one meeting with him, Superman finds the new Brainiac is more frightening than any other of his enemies.
Superman:Besides, this new Brainiac frightens me...He's unlike any enemy I've ever met before. He has no morality, no compassion— He simply wants to control. And I don't know if even a Superman can stop him!
Even other Superman-level villains such as Mongul, Zod, and Non are terrified of him. In "Superman: Doomed", Mongul even opts to hide in the Phantom Zone if the alternative is being in Brainiac's way.
Doomsday killed and gave Superman nightmares after his resurrection. The beast is nothing more than a rampaging force of nature that will kill anything because he's been genetically designed to treat anything as a threat. He's torn through an iteration of the Green Lantern Corps, two iterations of the Justice League, an iteration of the Suicide Squad, and even Darkseid. When heroes face him, the only thing they can hope for is either Superman showing up or a quick death. When Superman faces him, he hopes he can put him down fast enough to keep the body count very low.
Supergirl Adventures Girl Of Steel: General Zod "the Conqueror" overthrew the Argo council in a violent coup and began a decade-long which earned him monikers such like "the Merchant of Death" and "the Butcher of Argo" until he was finally captured and thrown into the Phantom Zone. Three hundred years later he is still a boogeyman to Argoans like Supergirl, who flies off when she bumps into him (in order to come up with a working strategy).
Amanda Waller in 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."
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, that's if a very well done theory video made by The Imaginary Axis is wrong and he ISN'TEvil ITSELF. 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. In fact, even Superman and other more moral members of the Justice League are fine with using lethal force on him.
In Legion of Super-Heroes storyline The Great Darkness Saga, the Legionnaires were already frightened of the Master of the Darkness before knowing who he was. After Brainiac figures out the Master is Darkseid, the Legion goes from "Uh-oh" to "Oh, CRAP!".
Dream Girl: "We were frightened of him before we knew who he was, Sun Boy— unfortunately, there's more reason for fear now."
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 as part of Villain's Month during Forever Evil (2013), 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.
Darkseid's father Yuga Khan is considered even worse than he is. When he briefly escapes from his imprisonment in the Source Wall, even Darkseid cowers before him.
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 Lanterns' 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.
And of course, Sinestro himself. During "Green Lantern: Rebirth", it's mentioned that Guy Gardner, who will mouth off to Batman and Wonder Woman, tends to mock pretty much all of Hal's old enemies. But he never makes a crack about Sinestro.
Teen Titans: Trigon Raven's dad and an interdimensional demon lord who can only enter the real world through her psyche. He is this from the perspective of the Titans and the people of Azarath anyway with good reasons.
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.
Doctor Manhattan has become this in DC Rebirth, where anyone even remotely able to alter reality is scared shitless of him and will flee at the very idea that he'll show up.
Secret Six: Junior 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.
Bart Allen, aka Impulse, serves as this to Superboy-Prime due to handing the near invincible villain his first defeat. Said defeat doesn't just leave Prime terrified of Bart to the point that he will flee rather than face the speedster, but he's also moderately phobic about speedsters in general.
When it comes to the many alien foes the Justice League has faced over the years, few elicit such a guaranteed "oh shit" moment than Despero. He's a bloodthirsty juggernaut with a wide range of Psychic Powers plus a mind that knows how to use them properly, all of which is tempered by cold, sadistic fury and hatred. When he shows up, holding back is not an option, and it always takes multiple teams just to slow his progress. A single team going up against him is a suicide mission.
Wonder WomanVol 1: During Marston's run the Holliday College Dean terrified friend and foe alike, with General Darnell fearing losing her spy/students on missions mostly because it would bring her anger to his door. With the Holliday Girls—a pseudo sorority espionage and adventure group—their fear of their Dean was usually played for laughs, but the occasional villain that made the mistake of running into her not knowing any better learned their lesson quickly. Many of those scared of her were unaware she was anything more than an old woman and college dean, as her school's spy activities were secret.
