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.
However, one criminal recounted he moved 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?".
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 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 in 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.
The Scarecrow! Even though Dr. Jonathan Crane may appear to be a hapless dweeb or a schmuck villain, he's just as dangerous of a threat to Batman himself. There is a reason why he dubs himself the "MasterofFear".
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.
Judge Fear is made of this trope, quite literally too;
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 resurrected Darkseid. The Oh Crap faces they all make speaks volumes.
On a more humorous note, the tiny alien dragon Lockheed is this for the Brood.
Subverted by Venom, the Evil Counterpart to Spider-Man. In his heyday, Venom was widely feared in the supervillain community, although this was typically due to how well he did against Spider-Man. On the other hand, he got his ass kicked by C-listers like the supervillain Styx and the superhero Darkhawk. Fridge Brilliance kicks in when you remember that Venom had some major advantages against Spider-Man. He knew Peter Parker's secret identity, which meant he could torture Peter in his civilian identity as Eddie Brock, and he was also immune to Peter's spider-sense, which screwed with Peter's usual fighting style. When he goes up against someone like Darkhawk, who's not psyched out by Eddie Brock and whose powers are not hindered by him, Eddie loses all his trump cards and becomes a much weaker foe.
Though being a stronger version of Spider-Man, who unlike Spidey is perfectly willing to kill, is in and of itself rather formidable.
In Gold Digger, Dreadwing is the most hated villain in the series. He doesn't even have anyone under his command 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 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 hates him, the more powerful he becomes.
The Punisher, foreveryreasonyoucould believe. The very mention of the name "Frank Castle" is enough to scare the bejeezus out of the toughest, meanest thugs, killers, and mafiosi. 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.
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 developent a mythic reputation on some planets who have tried to invade Earth, only to be challenged by them and have their asses kicked; the culture 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 Heralds.
While not explicitly mentionned 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. 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. 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.
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 Hulk blood sample in an attempt to cure his ailing abilities. His reaction was to talk him up using the lyrics of his old cartoon theme song ("Ain't he unglamorous").
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 supergenious but still smart), has no qualm in 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.
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 justified by the fact he is insane, and evil, sadistic, psychopathic... and equipped with the power of the Chaos Emeralds.
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. When he briefly disappeared (thanks to Magneto's attempt on his life), his return caused Captain America to have a temporary Heroic BSOD.
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 Nazi. At which 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.