The 100 has a group of creatures called "Reapers", a race so terrifying that even The Grounders, a tribe of hardened warriors who were trained on a hostile Death World, avoid them like the plague.
Agents of S.H.I.E.L.D.: Ghost Rider. Everyone is deathly afraid of him, from a combination of the fact that he's powerful as all hell (literally), a cold-blooded and merciless killer, and that virtually nothing is known about him, especially concerning his seemingly inexplicable powers. Coulson's team puts on a brave and commanding front, but even they know he's a time bomb best not set off. Coulson sells his continued participation to Director Mace as, more or less, "nothing we have can stop him."
Has The Destroyer, a very powerful creature transfer over from the hell dimension Quor'toth, who is revealed to be Angel's son Connor.
Angelus, the Super-Powered Evil Side of Angel. When the Big Bad from season 1, a very old and evil vampire in his own right, describes him as "the most savage creature I've ever met"...
Every employee of Wolfram & Hart is extremely afraid of any actual contact with a Senior Partner; they signed up to work for them as an absentee boss, but it's horrible when they come to this dimension personally. This forms most of the plot of the episode "Reprise," and in "Deep Down," even the CEO Linwood Murrow knew he was done for as soon as Lilah started bragging about having had a personal audience with a Senior Partner.
Even before he actually showed up, the show established that Bigger BadRa's Al-Ghul is so frightening that everyone who knows of him is terrified of him, even Season 1 Big Bad Malcolm Merlyn. And when he does finally show up in Season 3, it becomes clear that his reputation is not only well-founded, but an understatement.
Season 2: Slade Wilson aka Deathstroke also invoked a lot of fear, to the point that Oliver and Sara, two of the biggest badasses on the show, are utterly terrified when they realize he's in Starling City. Even Amanda Waller was reduced to tears when she found out he was alive.
Damien Darhk has such a reputation in the magical (under)world that even John Constantine was wary of him and told Oliver to be careful with this one.
Prometheus. Everyone but Team Arrow is scared of him, and that's because Team Arrow hates him to the very core.
The Reverse-Flash, aka "The Man in the Yellow Suit", to those who know of his existence. Barry himself admits that he fears as much as he hates the Reverse-Flash, and it's that fear that has prevented him from leaving Central City and moving forward with his life.
Zoom. Earth-2 lives in such sheer fear of him that the police don't even bother opposing him anymore. He quickly became similarly feared on Earth-1 after he outright crushed the Flash in their first fight. It's implied that even the Season 1 Big Bad fears him, judging by how he took the appearance of Zoom's helmet as his cue to leave.
Tombstone is perhaps the most iconic bot of the ABC series, and for good reason. Its main weapon is a massive spinning blade with immense destructive power. Most robots win fights by hitting the other robot until it stops working. Tombstone wins fights by hitting the other robot until it isn't in one piece anymore. Tombstone was feared enough that despite not winning Season 1, it was given the top seeding in Season 2, which ended in Tombstone claiming victory. And every battle it fought in Season 2 until the semi-finals was won by knockout.
Minotaur is giving Tombstone a run for its money, with a weapon that is similarly destructive, combined with the robot itself being small, fast, and very durable. Its own weapon sounds like a jet engine revving up, and left a trail of destruction in its wake comparable to Tombstone.
Breaking Bad: After the murder of Gus Fring, Walter White, by the name Heisenberg, is known and feared throughout the American southwest.
Jesse Pinkman also became feared for a time after the death of Spooge, who had stolen money from one of Jesse's friends. Of course, he didn't actually do it, and he became not-so-feared once Spooge's girlfriend fessed up to his death.
Buffy the Vampire Slayer: The big bads tend to be this to the heroes and usually for a really good reason. With the exception of Angelus in season 2 (who was himself quite strong and had an almost foolproof plan) all of the villains have been nigh unstoppable, cunning and highly destructive.
Buffy herself is this to the monsters.
Lothos. He was famous for killing many past Slayers. Consider that Spike was considered a Badass Nonhuman for killing two.
The Master. In the Dreamverse, his escape from his can is one of Buffy's darkest nightmares and preventing his escape is Angel's top priority. The unspoken belief between them is that they won't be able to stop him if he gets out.
Angelus, despite not being as strong as the other villains, definitely qualifies as this.
The Mayor, perhaps not to the same extent as Angelus or The First but it is worth noting that he was able to freak out both Mr Trick and Deputy Mayor Alan Finch, and had control over his own personal army of vampires before he became invulnerable. Hell, he even freaked out the Scooby Gang when he casually walked into the library.
Severin is the prophecied Siphon, whose coming had long been feared among the magical community.
Faith is nine kinds of panicked when she sees Kakistos again, with Buffy even mentioning in Buffy the Vampire Slayer: Chaos Bleeds that he was the one thing Faith was ever truly terrified of. Furthermore, his reputation is such that Giles immediately recognizes his name when Buffy, being Buffy, misidentifies him as "Kissing Toast."
The main character develops this kind of reputation over the course of his spy work before the series starts. One agent admits his agency always assumed "Michael Weston" was just a code name for a group.
"I'm Michael Westen... yeah, that one."
In fact, Michael is considered a boogeyman to Russian special forces that when he told them his name, they backed right the hell down.
The Cape: Chess is this, the mere mention that he could possibly be alive being enough to spook public defender Dana Faraday.
Cheers: Norm became this in one episode, when the CEO of his company forced him to become the company's hatchet-man, essentially giving employees notice that they had been laid off. At the end of the episode he decided he could not keep this job with a clean conscience, so he decided to turn in his resignation. He tried calling his immediate supervisor and then the CEO's secretary, both of whom hung up immediately; word had gotten out through the company grapevine that if you got a call from Norm Peterson, it meant you were being laid off. When he realized what was going on, he called up the CEO personally and greeted him with, "Hello, sir? This is NORM!PETERSON!MUAA-HA-HA-HA-HA-HA!"
Two words: Wilson Fisk. Until episode 3, he's an offscreen menace who has only ever interacted with people using James Wesley as his intermediary. After Matt Murdock defeats John Healy, he tries to squeeze a name out of him. Healy reveals Fisk's name, then promptly impales his face through a fence spike to keep Fisk from going after any of his family.
Frank Castle becomes one through the start of season 2. He is known to inflict cruel vigilante justice on those he comes across, and is scarily competent at tracking down targets no matter what they try to do to throw him off their trail. Matt might break a few bones and smash up your operations but Frank will send you to your grave without a second thought. This also makes him this to the police, since he can start gang wars by himself. In fact, in Luke Cage, one of Blake Tower's arguments against arming ESU cops with the Judas bullets is because it's possible that a guy like Frank Castle might get his hands on it.
Dexter: When one of George King AKA 'The Skinner''s employees is brought in for questioning about a series of murders, he has a near panic-attack, and would rather go to jail than convict him, and for good reason.
The Daleks are treated by all who know them as the bogeymen of the Doctor Who universe. Even the Doctor, who's battled and defeated them uncountable times, always treats their arrival with a mixture of grim determination and just plain old fear.
Best seen in the end of the first part of "The Stolen Earth". When the first broadcasts of "EX-TERM-IN-ATE! EX-TERM-IN-ATE!" reach Earth, the former companions and allies of the Doctor such as Sarah Jane, Martha Jones, and even Jack Harkness — some of the bravest people in the universe, one of whom is outright impossible to kill — are stunned into a state of tearful panic.
When the Daleks are first encountered in the new series (in the eponymous episode "Dalek"), the Doctor reacts with sheer panic when he realizes the alien prisoner he is locked in with is (apparently) the last surviving Dalek.
After the reboot of the universe, Rory Williams has been interwoven into the myths and legends of human history as "The Last Centurion". Woe betide anyone who threatens his loved ones;
When they first appeared in "The War Games" the Time Lords were treated as this by the Doctor and the War Chief.
Should be noted, before certain events in Series 7, The Doctor qualified for this trope. In that his name and history was enough to terrify plenty of alien races. Including, irony abounds, the Daleks. The only thing that gives a Dalek pause is the Doctor's name. The only thing that scares them is a madman with a box, the one presence in the cosmos they would not wish to face. In fact, this is made especially clear in the Series 5 episode The Pandorica Opens. The Doctor's enemies have designed a perfect prison to trap the Doctor in. Considering that, the legend surrounding the Pandorica reflects on what his enemies think of the Doctor:
The Doctor: There was a goblin. Or a trickster, or a warrior. A nameless, terrible thing, soaked in the blood of a billion galaxies. The most feared being in all the cosmos. And nothing could stop it, or hold it or... reason with it. One day it would just drop out of the sky and tear down your world.
Even the Doctor's incarnations face this. There is an incarnation those following the Eighth Doctor don't speak of: the War Doctor. He is notorious for breaking the promise bound to the name "the Doctor" by burning down Gallifrey and the Daleks with them. note Of course then it's found out in the 50th Anniversary special that Gallifrey didn't burn and was instead preserved in stasis by all of the Doctors (It Makes Sense in Context), and the only reason the timeline still asserts the War Doctor as The Dreaded is because he and Ten forget they actually saved Gallifrey after they return to their own times.
Gallifreyan Soldier: First thing you notice about the Doctor of War is that he is unarmed. For many, it's also the last.
In "The Day of the Doctor", we are treated to two back-to-back encounters of The Dreaded: first, as a group of Daleks invade Arcadia, the second city of Gallifrey, a swarm of the Omnicidal Maniacs surrounding a group of unarmed, defenseless Gallifreyans, including scared, crying children, and then we get the second, as, before the Daleks can slaughter these people, they all detect the presence of the Doctor, and dare not waste even a minute fraction of their attention on anything but their long-hated foe, with not even one staying behind to finish off the helpless people.
A major reason why Tywin Lannister is so feared is due to his control over Gregor "The Mountain" Clegane, who is so notorious for his almost inhuman size and strength that even certified badasses fear to face him (and, to a lesser extent, his younger brother Sandor "The Hound" Clegane). Actually, a majority of the Lannister soldiers are portrayed as absolute monsters who use fear and violence to achieve goals.
After Flaying Alive a lord who didn't submit to his father's rule (as well as his wife and brother), Ramsay Bolton becomes feared throughout the North, and people are now submitting simply to avoid his horrific reprisals, a reputation he is clearly pleased with. His father on the other hand, despite the submissions, is less than pleased due to the long-term problems of dealing with bannermen in this manner, because it means that Ramsay is hated as well as feared. Sansa ends up running away in large part out of fear of what Ramsey could do to her, which as Roose points out, would invite rebellion from the North, and the wrath of the Iron Throne.
Stannis Baratheon has a reputation as a humourless and merciless determinator and his resume includes holding Storm's End against all the power of House Tyrell with 500 men while being Reduced To Rat Burgers, storming the Targaryen island bastion of Dragonstone, smashing the ironborn fleet at Fair Isle, and subduing the island of Great Wyk. And that's just his Back Story...
The Blackfish's status as an in-universe memetic badass means Roose Bolton is quite concerned that he may have survived.
The ruthless cutthroat Karl Tanner claims he was once known as "The Legend of Gin Alley," and definitely terrifies his companions.
The Iron Bank is infamous for funding the enemies of states and rulers who default on their loans. Tyrion is unnerved to learn Littlefinger has sunk the realm millions in debt to them and Olenna calls Tywin's bluff when he claims he's not worried about it, saying he's too smart not to be worried.
When Arya Stark confronts Melisandre, the red priestess seems to think so of Arya, being somewhat terrified of the sight of her. This is because she sees and knows what Arya will become.
Just Grey Wind's growls are enough to put Jaime Lannister on edge and Lannister troops tell chilling stories about him.
Grimm: The Grimms are The Dreaded of the Wesen world. Whenever someone realizes Nick is a Grimm for the first time, they are terrified and often beg not to be killed. Monroe explains it best;
Monroe: You're the monster under the bed! [...] You're not real! You're a scary story we tell our kids! Be good or a Grimm will come and cut your head off...
And like Harry Dresden or the Doctor, he's beginning to earn a reputation for himself one encounter at a time as people get wind of what he went up against and what the outcome was. He'd deny being one of the baddest badasses out there, but the scorecard says he is.
It helps that there seems to be something about Grimms that makes Wesen instinctively fear them. Many badass Wesen who never encountered a Grimm before, are paralyzed with fear the moment they see that Nick is a Grimm. It seems to be a supernatural element of being a Grimm but it has not been explained on the show.
Partially explained in Season 3, that when the Wesen woge they see the Grimm's eyes turn black and their true selves reflected in them.
Heroes: Sylar. When a gaggle of supervillains are released from their cells and have the chance to take revenge on Noah Bennet, the guy who locked them up, Noah only has to say one thing to scare them into teaming up with him: "Sylar's in the building."
Bennet was pretty dreaded himself at first. He's a Badass Normal who used to work for The Company and was very good at it. Sylar is in fact the only thing more feared than "the man with the horn-rimmed glasses." In fact, when an eclipse robs all of them of their powers for a few hours, Sylar has to run and hide from Bennet, who suddenly has the upper hand (well, a sniper rifle).
Another rare game show example: In Jeopardy!, there is a category called "The Dreaded Spelling Category", and it is dreaded, because the contestant does have to spell the word, exactly. (Not as easy as it seems.)
"The Dreaded Opera Category," as well, because very few people know it well enough to do well on it. Naturally, this was always saved for last.
On Justified Theo Tonnin, The Don of the Detroit Mob, is portrayed like this. He has been the head of his crime family for over 30 years and the cops can't get any charges to stick. According to stories he likes to travel with a severed human ear in his pocket and if he pulls it out and starts talking to it, you know that he is really angry at whoever he is currently with. His mob lieutenants are shown to be Axe-Crazy psychos but they all adore/fear Theo and he manages to keep them in line (most of the time). This portrayal is helped by a large dose of Real Life Writes the Plot since the actor portraying Theo is very busy and could only appear sporadically on the show. The writers had to invent other mobsters to act as the Big Bad of a season which resulted in Theo being portrayed as someone even those guys are deathly scared of.
Human Target: Guerrero has managed to interrogate people just by introducing himself. Of course, being prime time they have to keep most of the stuff that got him the reputation off screen.
Kamen Rider Kiva: Wataru develops into this after recovering from his Heroic B.S.O.D., as demonstrated where he begins sends Fangires fleeing in terror simply by staring them down. Without transforming into Kiva.
To clarify, after having kicked much monster ass since 1971, Riders themselves are now dreaded. When Shinnosuke suits up for the first time, and the Roidmudes a good look at what his suit looks like, they and their bosses start taking him very seriously because they're dealing with a Kamen Rider now, and you don't screw around with one of those! As per the downplaying of the title's use in the revival era, Drive is initially just Drive, and in fact had never heard of the term until he hears the bad guys decide he's one and get scared. He decides it's pretty cool and he'll be "Kamen Rider Drive" now.
Even more clarification, in this series the villains plans to freeze time around the world were thwarted by a single Rider in a single night leading to the dread.
In Leverage, Eliot Spencer is a rare heroic example. Anyone who knows Eliot's reputation as a supreme badass takes him very seriously. When he announces himself by name to Moreau's bodyguards, an entire roomful of people draw guns on him and the closest ones actually look worried. Later on, Eliot proves they were right by mowing down a warehouse full of those same bodyguards by grabbing guns for the first time in the series.
Merlin: Merlin's older alter-ego has this reputation towards Morgana in series four. While a heroic example, he's not a Terror Hero as this is completely unintentional on his part, and she's terrified because the gatekeeper of the spirit world told her that he is her destiny and her doom. Whenever she sees him in his aged form, she has Tears of Fear. It doesn't help that he commanded a dragon to burn her army, stripped her of her powers once, and in a magical battle, completely curbstomped her and tossed her aside like a rag doll.
Morgana's vision of the future plays this straight. She's lying wounded on a battlefield, littered with the remains of her dead soldiers. And then we see the older Merlin, standing over her triumphantly and seemingly all-powerful, furiously admonishing her for all of her crimes.
Merlin: Is this really what you wanted, Morgana!
Monty Python's Flying Circus: Everyone in London is terrified of Doug Piranha, including his brother and partner in crime Dinsdale. "I've seen grown men pull their own heads off rather than see Doug," Luigi Vercotti says. Doug's most horrifying technique? Sarcasm.
Mr. Young: In the first episode, Derby describes Slab as a cross between Godzilla and Bigfoot. This becomes a plot point in "Mr. Hyde" when Adam develops a serum that makes him more confident, but also turns him into a monster whenever it takes effect, but finds that just looking at Slab scares him enough to turn him back.
Regina is feared by the citizens of Storybrooke, as is Mister Gold, for good reasons: Regina is the Evil Queen herself, a powerful sorceress who, while being deprived of her powers while the curse is still effective, has powerful connections and a tight grisp on her town as the mayor, and Gold is Rumpelstiltskin, who practically owns the place. Rumpelstiltskin in particular was the most dreaded of all, thanks to his powers as the Dark One in the fairy tail land.
Starting season 2, another character shows up who even Regina and Gold fear: Cora, Regina's mother, who is even more powerful than her daughter. Gold himself is willing to take extreme measures to make sure that she won't travel to Storybrooke (when the resident Magnificent Bastard and The Chessmaster of the show is scared of someone, you know things got very serious). The icing on the cake? She is the Queen of Hearts from Wonderlands. You may now panick.
Season 3 introduces the most unexpected character as the new Big Bad of the story, who also turns out to be absolutly amoral and feared by all: Peter Pan. Which lead to a very interesting Enemy Mine situation in which characters who previously hated eachother to death are now teaming up together against him in order to save Henry. Considering how mischevious, smart and manipulative Peter Pan is, cooperation is mandatory.
Once Upon a Time in Wonderland: While Jafar is absolutly merciless and feared by most, turns out there is another being who is frightening enough to make all wonderland citizens have a massive "Oh crap" moment when they realize it is released: the Jabberwocky, whose weapon is literally fear, and who is a master of Mind Rape. It will enter your mind, dig up your most secret fears and use them against you, making you wish it would just stop. The thing is, it doesn't even need to get physical: by just making you relive your fears, it can kill you. This creature is the master of Break Them by Talking speeches. You can't escape it. You can't hide your fears and most dark secrets. Once it gets a hold on your spirit, you are done, defenseless. And even if you somehow manage to fight back, you will soon find that it is useless, as the Jabberwocky is immortal, and there is only one weapon out there that can stop it. Sleep well.
"The Originals": It's been shown that the Mikaelson's very name is enough to make even older and violent vampires go pale and they more than back it up (especially Klaus) to ensure that if you cross them, you die very, VERY violently.
Twin Peaks: Bob. An evil spirit that raped and murder Laura Palmer. Possesed Leland and murdered Maddi.
Chaos 2, a Lightning Bruiser robot which zipped around at 20mph and was armed with a high-pressure air flipper that sent opposing robots Blown Across the Room. Curb Stomped every single opponent it faced in Series 3 and 4, and for nearly all of Series 5 until it was defeated by Bigger Brother. 24 wins, 9 losses, and the only double champion in the show's run.
George Francis: If you know anything at all about Robot Wars then you already know who we are.
Hypnodisc, a robot named for a huge spinning disc which served as its weapon. Notable for literally ripping enemy robots to shreds. Its first fight ever had it inflicting, in the words of commentator Johnathan Pearce, ""the most complete destruction I think we've seen on Robot Wars ever." 22 wins, 12 losses.
Peter Kinsley: We did not want to meet Hypnodisc... This machine was stunning for the amount of damage it dished out. The pits were very quiet when it was on.
Carbide became an absolute terror during Series 9, with a spinning bar that packs the same steel-rending capability that Hypnodisc used to have paired up with flipping resistance and a few upgrades that made it surprisingly unkillable for a thing that deadly. A Glass Cannon that covered its glassy weaknesses, it tore right through everyone during that series, and came out completely undefeated, with opponents being increasingly afraid of that unnerving hum that came from its bar gaining enough speed to rip its foe to pieces. That is Not Hyperbole, in at least one fight bits of the unfortunate adversary had to be pulled out of the plexiglass walls.
RunningMan: Everytime Choi Min Soo is a guest star, the show becomes terrifying.
Played for Laughs with the Janitor from Scrubs. Two different episodes show he has a crowd of people who do whatever he wants out of fear. He even invents a new word to describe himself: "fearitude".
Theokoles, the Shadow of Death. This giant, undefeated gladiator terrifies everybody when he's announced to be coming out of retirement. Everyone assumes that Spartacus and Crixus are doomed when they are announced as his opponents.
The Borg Collective in various series. Despite appearing rather infrequently in the series where they first appeared, their sheer implacability, utterly relentless nature, and single-minded goal to assimilate everyone and everything that they come across led to The Federation considering them, as Captain Picard puts in Star Trek: First Contact, "our most lethal enemy". Even Guinan is afraid of them, what with them having assimilated her home world. The suspense that builds up around their incursions into Federation space is particularly indicative of this. It's less so in Star Trek: Voyager, where Voyager encounters them so frequently without being in much danger that the Borg end up exhibiting Villain Decay.
In the first season of TNG, the Ferengi were treated this way. It didn't last long.
A non-villanious example is Lwaxana Troi, Deanna Troi's mother. The crew of the Enterprise become very nervous whenever she arrives. Captain Picard, in particular, fears her, once hiding in a holodeck to avoid her and another time being tricked into taking a vacation when Counselor Troi lies about her mother's impending visit.
The Iconians were so feared that the other races in the galaxy banded together to wipe them out via orbital bombardment of their homeworld and called them "Demons of Air and Darkness". In Star Trek Online, the Iconians turn out to be not so extinct and they are responsible for the strife plaguing the sector. In their first appearance, a single Iconian casually vaporizes six people with a wave of her hand, before . Furthermore, the Dominion is so afraid of the Iconians that their official policy for dealing with them is to give the Iconians anything and everything they want, hoping they will go away.
M'Tara: We give you a single warning: do NOT attract our attention again.
Star Trek: Deep Space Nine: Dax is notorious among Trill initiates for being one of the worst mentors for an initiate to be assigned to. Dax is infamous for have broken more initiates (thus ending their chance of becoming Joined Trill) than any other Joined Trill. Being assigned to Dax is therefore regarded as practically a death sentence by most Trill initiates.
A variation occurred in the Star Trek: The Next Generation episode "Face of the Enemy", where Troi was kidnapped by a Romulan underground movement, and subjected to surgery so she could assume the identity of an operative in the Romulan Tal Shiar named Major Rakal. (The real Rakal had been covertly killed by members of the movement for this very purpose.) Troi quickly found that other members of the Romulan crew were terrified of her because of the reputation of both Rakal and the Tal Shiar; apparently, they have the authority to execute other Romulan officers for any reason they see fit, and are quite liberal (and at times cruel) with this privilege. (In fact, that's the exact reason resistance member N'Vek chose her for the part; he thought that she could play the role well and not give herself away, and in fact, they never suspected a thing until it was too late, with N'Vek making a Heroic Sacrifice to finish the mission and get Troi back to the Enterprise.)
Khan Noonien Singh is cited as the sole reason for the Federation's No Transhumanism Allowed policy. In the 1990s Eugenics Wars, he was able to take over at least a quarter of the Earth, managed to escape to space when normal humans deposed the other supers, and later proved a match for James Kirk, Starfleet's resident Memetic Badass. Even a century after his death, Starfleet is still absolutely terrified of another Khan rising from illegal genetic engineering programs.
Everyone aside the Klingon thread lightly when dealing with the Romulans, even if their schemes rarely obtain something. We see exactly why in two occasions:
In the original series, a single bird-of-prey, fusion powered (compared to the Federation's use of antimatter as fuel) violating the Neutral Zone sent the Enterprise's crew in Oh, Crap! mode before they realized the little ship actually outgunned the larger Federation vessel. Kirk has to use all its wits to take that one down...
In Deep Space 9 the Dominion apparently plans to deal with the Federation and the Klingon at the same time before getting in a war with the Romulans. Then the Federation tricks the Romulans into thinking the Dominion plans to attack them... And, a few weeks later, the Romulans have single-handedly beaten the Dominion forces back in the pre-war Cardassian space, before actually bothering to contact their new allies-partly because they have to give them back the worlds they liberated.
Supernatural: Has a few depending on the season. In the first season, demons are nigh-unstoppable. In the first episode with one, Sam and Dean have serious trouble exorcising a single demon—it could be anyone, conventional weapons are all useless (the only thing that can hurt it is holy water), and, to kill it, they have to enable it to posses the plane itself. When they learn it was a demon that killed their mother, they become very unnerved. Once they get their hands on the Colt (a gun that can kill anything) and learn how to make devil's traps, demons become a lot less threatening, though are still highly feared, until...
Season 4 shows that angels are this to demons: a group of demons harass Sam and Dean shortly after Dean is mysteriously brought back from Hell, but Sam points out that the demons don't know how Dean is alive, either, and are more afraid than they are, because it means there might be a bigger fish. Later, Sam goes back to kill them and finds that their eyes were burnt out because they saw what it really looked like. The only survivor is gibbering about how the end is upon us and how everything is going to die. When it turns out that nothing Sam and Dean have or can do will hurt an angel and sometimes angels can go bad and/or insane, things escalate quickly. Upping the ante from there, regular angels fear archangels, who can smite their lesser brethren into nothing with apparently little effort.
Season 7 ups the ante with the Leviathans, who can regenerate from just about anything, shape-shift into someone perfectly (as long as they have a tiny DNA sample), tear through just about anything and anyone, are immune to angels, demons, monsters, Eve, weapons (can't hurt them permanently), fire, iron, salt, and silver. The only things that can hurt them are...Borax-based cleaning products. Decapitation slows them down, but they can only be killed by being eaten by another Leviathan, being forced to eat themselves (used as a punishment for failing their leader), or being stabbed by a "bone of a righteous mortal, soaked in the bloods of the three fallen" (a fallen angel; "the father of fallen beasts", an Alpha; and "the ruler of fallen humanity", the King of Hell). The head Leviathan is this to his subordinates, as his very name is enough to make them shake in their boots. He plans to kill every monster, demon, and angel he can and change human physiology—to make us live longer, be more disease resistant, and much fatter—and psychology—to make us passive—so the whole planet becomes a buffet for the Leviathans.
Hellhounds. These mutts even scare angels, and for good reason. Once they're sicced on someone, that someone is screwed. They're invisible, super-strong, nigh-invulnerable, and never, ever stop hunting their prey. After being introduced in season 2, they were the harbinger of doom: when they appeared, a character was going to die messily, and the heroes don't get to kill one until season 8.
Death tops them all. He is the only being in creation that can make Dean Winchester quake in his boots. One day, Death will reap God Himself.
The Winchester brothers themselves are becoming this to the supernatural community—mostly demons and angels, who know about all the stuff they've done.
Dean Winchester, even before... everything. Also,he killed Death.
Roy: Killing Sam was right but Dean...
Walt: He made us and we just snuffed his brother, you idiot. You want to spend the rest of your life knowing Dean Winchesterís on your ass? Ďcause I donít. Shoot him.
The Darkness is the epitome of this trope. Even Lucifer, the Archangel Michael, and Death himself seem afraid of her. Considering she's the source of all evil in the universe and equal to God in power, it's not surprising.
And speaking of them, Chris and Snoop also count. The two are the chief assassins of Marlo Stanfield, the most ruthless, sociopathic, and murder happy drug kingpin Baltimore has ever seen. Despite the fact that Snoop is Hot-Blooded and she frequently seems to be a wrong word away from killing someone, it's the calm and disciplined Chris who is more feared on the streets. Chris has such a reputation that in one scene a group of kids from the neighborhood speculate that he has supernatural powers.
Brother Mouzone is possibly an even bigger one than all the others mentioned. The mere thought of this guy being brought in to interfere with their plans scares the shit out of Stringer and Prop Joe.
Prop Joe: You think I'm going to send any of my people up against Brother? Shit, that man got more bodies on him than a Chinese cemetery.
Though, to be fair, only certain people (like Joe and Stringer) seem to know who Brother Mouzone is. Omar, apparently, didn't know him. Cheese suffered a great deal of pain and humiliation for his ignorance.
Stargate franchise: The Goa'uld are usually this to most human civilizations. The likes of Sokar and Anubis are feared even by other Goa'uld, and until Anubis upgraded their technology in season 6, they were all afraid of the Asgard. The Wraith and Ori also have this reputation.