Night Wizard features a Journey to the Center of the Mind, where the Band of Brothers faces off against a Devil-Queen of Nightmares who preys on dreams and devours the minds of the sleepers. Inside the mind of Elis Shiho, the mild-tempered Friend to All Living Things / MacGuffin Girl, she is defeated... but manages to survive and hide out in a weakened state, determined to bide her time as her powers return so she can seek vengeance. While looking for a good place to hide out, she finds a strange, black door in the dreamscape, and goes inside... followed by a Stock Scream, and her running wild-eyed out of there on the verge of a complete breakdown. What could possibly exist in the mind of such a nice girl, that is capable of terrifying a creature that lives off nightmares?
Tanaka Punie of Dai Mahou Touge is scary in ways that defy categorization. She activates this trope when she takes on a huge Dark God/Demon-thing... with wrestling-techniques. As soon as it realizes who she is, the huge beast is terrified and flees screaming back to the other realm.
The first act of true Badassery in One Piece is when Shanks scares off a giant sea serpent just by looking at it. It's revealed that he actually used his Haoshoku no Haki.
Toriko can do this. His intimidation is such that it can quell a herd of angry, monstrous apes.
In Hellsing the Ax-Crazy murderous vampire Rip Van Vinkle completely falls apart from fear when she just senses that Alucard approaches.
Alucard loves doing this. He really seems to enjoy knocking lesser monsters off their high horses.
Luke Valentine (a powerful vampire himself): What are you!? WHAT IN THE HELL ARE YOU!?MONSTER!
In The Slayers, dragons and many demons are absolutely terrified of Lina Inverse. When she gets a letter from her older sister Luna, Lina freaks out, trying to hide in a pyramid.
Many horrific creatures are scared shitless of Doc Stearne, aka Mr. Monster.
Doctor Doom fears nothing!...Except for Squirrel Girl. When she shows up to borrow his time machine, he just lets her have it, with a caption reaffirming that their previous encounteris canon. Deadpool finds her terrifying as well. In fact, she's slowly gaining a reputation as The Dreaded among Marvel's villains.
Used in a plot arc in DC's old Forgotten Realms comic. The dragons of Faerun are generally badass, aloof, and most if not all of them have killed plenty of "lesser" beings before for some reason or other...but even they have a collective Oh Crap moment and are earnestly considering leaving their familiar home grounds behind and moving into places more commonly populated by humans, elves and so on when a mysterious killer starts to leave a trail of headless dragon corpses behind him-, her- or itself.
Time Braid has Sakura of all people pull this off. Orochimaru summons his Kusanagi and stabs Sakura in the heart then promptly freaks out when she ignores it to study the seal he uses to contain his sword.
In the theatrical cut, Anne is attacked by two lizards the size of tigers and crawls into a log to escape them. As she does, one is pulled offscreen and upwards by something, and the second stares at whatever it was and promptly beats it. Anne, exiting the log, finds a V-Rex standing there staring at her, the remains of the first beast in its mouth.
Aldo: We will be cruel to the Germans, and through our cruelty they will know who we are. And they will find the evidence of our cruelty in the disemboweled, dismembered, and disfigured bodies of their brothers we leave behind us. And the German won't not be able to help themselves but to imagine the cruelty their brothers endured at our hands, and our boot heels, and the edge of our knives. And the German will be sickened by us, and the German will talk about us, and the German will fear us. And when the German closes their eyes at night and they're tortured by their subconscious for the evil they have done, it will be with thoughts of us they are tortured with. Sound good?
In The Light Fantastic, Rincewind (the ultimate coward) ends up fighting a creature from the Dungeon Dimensions (where everything HP Lovecraft ever thought of lived), while it possesses a man that may be the most powerful wizard on the Disc at that moment in time. He fights it using nothing but his hands, feet, elbows, knees and teeth. In the end, the author points out that this is the first time anything has ever run away from Rincewind instead of the other way around. He not only beat up Cthulhu, he actually scared away Cthulhu with a fist-fight.
This comes up at the end of I Am Legend following The Reveal that not all of the vampires are mindless, bloodthirsty monsters. The vampire-hunting protagonist realizes that, to the vampires, he has become a terrifying figure, a myth of godlike proportions. Basically, he's become a legendary monster that vampires tell each other ghost-stories about.
In H.P. Lovecraft's Dream Quest to Unknown Kadath servants of Nyarlathotep, including (and especially) the monstrous Shantak birds are absolutely terrified of Nightgaunts, because they serve Nodens, Nyarlathotep's mortal enemy and the only being who really poses any kind of threat to him in the Dreamlands.
Early in Changes Harry comes face-to-face with a Red Court vampire. Keep in mind, a Red Court vampire can disembowel a half dozen mortal combatants in a matter of seconds, and this one in particular is one of the Court's best assassins. On seeing Harry, it shrieks in terror and bolts through a wall in the process of running for its life. Of course, over the course of the war, Harry has garnered himself a bit of a reputation.
As for the ghouls, well, one of them managed to get hold of two young Warden trainees that were being taught fire magic. After killing the one that abducted them by lighting its body fat on fire and dropping it down a mineshaft, Harry blasted a captured ghoul into a hole he created, buried it up to the neck (melting the sand into glass as he did so) and laid a trail of orange juice to a nest of fire ants. He only put it out of its misery after he realised the other trainees were staring at him in horror. The only surviving ghoul was left to take a message to its kind. Never again.
Perhaps topping his list of achievements in this category is the fact that Nicodemus, a several-hundred year old agent of evil who has bonded his soul with an honest to God fallen angel is actively terrified of Harry, seeing as Harry is apparently the only person who has come even remotely close to actually killing him...on two occasions no less.
Several readers have noted that a certain Black Court vampire mage has not been seen or heard from since Harry gave her a brief rundown of all the things he could do to make her unlife Hell, should she try to target his friends ever again.
At the end of Fred Saberhagen's Empire of the East trilogy, the demon-prince Orcus, mightiest of all demons and founder of the eponymous empire realizes just whatArdneh is, and what Ardneh's plan is, he flees screaming. Of course, by that point, it was much too late.
The Children in Galaxy of Fear, a group of somewhat sympathetic cannibals, are terrified of a creature they call the Imp. It's Yoda. They're willing to follow our heroes after giant knobby white spiders, but not where they think they've seen the Imp.
Say the name of John Taylor anywhere in the Nightside, and most of the things that go bump in the night will fall over each other trying to get on the next train to Swindon.
In Strata, the explorers end up capturing a demon, which proves itself to be rather uncooperative. Marco, a particularly unbalanced member of a species that's already Ax-Crazy by default, gets fed up with it. "You said you can read minds? Then read mine." The demon does so...and spends the rest of its time with the group absolutely horrified of the alien.
Rorge is a serial killer and his companion Biter is a cannibal. What scares them? Their cellmate, the Faceless Man Jaqen H'gar.
The witch known as The Ghost of High Heart is freaked whenever she sees Arya Stark.
Evil Sorcerer Melisandre is frightened of the lackwit jester Patchface.
Roose Bolton, head of the most ruthless noble family in The North, is wary about the cannibalistic inhabitants of Skagos Island.
The Ironborn aren't too keen about the Crannogmen.
Live Action TV
The Buffy the Vampire Slayer episode "Teacher's Pet". A vampire is scared off when trying to attack a seemingly harmless substitute teacher. She turns out to be a giant shape-shifting praying mantis.
Later on, Glory scared a few vamps away by basically existing at them. This was before we found out she was a god.
In the Doctor Who episode "The Girl in the Fireplace", when asked what monsters have nightmares about, the Doctor responds "Me".
He has a similar line when he's trying to reassure young Elliot in The Hungry Earth:
Elliot: Have you met monsters before? The Doctor: Yeah. Elliot: Are you scared of them? The Doctor: Nah. They're scared of me.
This has become one of the Doctor's specialties. After untold centuries of defending the universe against the Daleks, the Cybermen, creatures too varied to count and too disturbing to name...well, let's just say that a race of supremacist, immensely powerful, intelligent living war machines, murderers of untold billions upon billions of beings, with no other emotion left to them but hate, refer to him as "The Oncoming Storm".
By the beginning of season 7 the Daleks have added an even more revealing name for the Doctor: The Predator of the Daleks.
Rose: 5 million Cybermen? No problem. One Doctor? Now you're scared.
In the Angel episode "I've Got You Under My Skin", an ancient Ethros demon possesses a boy hoping to corrupt and steal his soul only to realize too late that the boy had no soul. Instead there was a dark void that trapped the demon inside the boy. All of the creepy antics during the episode were the demon's attempts to escape by getting its host killed, even if that escape meant death for himself as well. When the demon is finally freed of the boy and Angel is about to kill him, it calmly accepts death and warns Angel about the boy's true nature.
Ethros Demon: Do you know what the most frightening thing in the world is? Nothing. That's what I found in the boy. No conscience, no fear, no humanity. Just a black void. [...] I just sat there and watched as he destroyed everything around him. Not from a belief in evil, not for any reason at all. That boy's mind was the blackest hell I've ever known. [...] I know you bring death. I do not fear it. All I have ever feared is in that house.
Angel's son Connor is this to the demons of Quor'Toth, "darkest of the dark realms". They refer to him as "The Destroyer" and will break into other universes to escape from him.
In a halloween episode of Two and a Half Men the brothers are terrorized by a witch who appears to have real cursing-type powers. Charlie has just capitulated to her demands that he become basically a slave to her coven, after she threatened to make his manhood "a shriveled husk." Then their mother shows up, and the uber-badass witch recognizes her and is so terrified of her that she flees in a panic.
The idea of Grimms is that they traditionally hunt down the creatures on which the monsters of our bedtime stories are based, so all but the most dangerous of said creatures are naturally terrified of them. Played with slightly in that the second, (counting his aunt) Grimm we meet is a pretty nice guy who treats these Wesen like he would anyone else, but they still react to him like he's a serial killer because his ancestors lived up to that reputation.
Interestingly, the fact that Nick is a cop tends to calm down some of them, since they rightly assume that there'd be questions if suspects and witnesses suddenly went missing or were found dead, all connected to cases of the same detective. Adalind, whom Nick is forced to protect as a witness at one point, points out that if he kills her, it won't be a Grimm killing a Hexenbiest, but a cop killing a witness.
In a mundane example, most people in The Wire are terrified of the drug gangs that all but own the streets of Baltimore... and those gangs are scared of Omar Little, a shotgun totting stick up artist who only targets the drug dealers or their fronts for his robberies. Most of his victims immediately surrender rather than try to resist when Omar robs them, and the only ones who attempt to fight him are the Barksdales and Stanfield gangs, and both do so when they are the most powerful drug empire in town. Unusually for this trope Omar is a massively Sympathetic Criminal who wouldn't shoot or even rob anyone who isn't a gangster and a Friend to All Children.
At the end of Leslie Fish's Filk Song "Banned from Argo", a gang of Klingons land on Argo, see the havoc wreaked by the crew of the USS Enterprise, and turn and run away. Years after the original song was written, a Firefly variant was made, with the Serenity crew scaring off Reavers.
The Disturbed song "Fear" which is written from the perspective of the victim so now it's the criminal that is experiencing fear:
Reject, are you no one? Feel you nothing? You know I'll bet you think You have a good reason to be living In the limelight of the fortunate ones You're too weakened by the poison That they feed you in the living lie They don't believe you: Call to no one Trust in nothing, Little impotent one
In the Deadlands universe, the Undead are animated by evil spirits called Manitou. However, the uber-undead Stone is such an evil son of a bitch, that his resident manitou is afraid of him.
Although they're loathe to admit it, the forces of Chaos in Warhammer 40,000 are all at least a little unnerved by the Necrons. Because they have no souls, only badly degraded digital copies of the personalities of long dead aliens, they're immune to most Chaos powers and any sorcerer trying to read their minds only sees an empty void. They also have a similar problem with the Tyranids, only in reverse. The mental and spiritual energy of the Tyranid Hive Mind is so overwhelmingly powerful and, more importantly so utterly alien, that it tends to disrupt the energies of the Warp, which are drawn from the souls of normal sentient beings, that give Chaos sorcerers and daemons their power. Often fatally.
It's implied that one of the reasons the Tyranids are invading the galaxy is because they are fleeing from something worse.
The Chaos God Malal. To wit, the other four Chaos Gods and their followers blankly refuse to associate with him. Malal is a Chaos God that wants to destroy everything, absolutely everything, including Chaos itself. There is absolutely nothing rational about anything the batshit loopy thing wants, but it doesn't let that phase it at all.
The Dark Eldar pale at the idea of offending or otherwise pissing off the Harlequins, and dare not refuse them entry to their otherwise impregnable inter-dimensional city, even if the Harlequins are just there to put on a show. Note that the Dark Eldar are psychotic hedonists who consider rape and torture to be nothing more than fun past-times. Monster Clown taken Up to Eleven.
In the end of MOTHER, the protagonists use Maria'slullaby to defeat Gyiyg, an alien Eldritch Abomination whose very presence has thus far thrown the world into chaos. As the song grows nearer to completion with each iteration, Gyiyg is reduced to screaming incoherently for the protagonists to stop.
In Star Control 2, the Ur-Quan are a race of slavers who want to control or lock away every other sapient race (Kzer-Za) and outright omnicidal maniacs (Kohr-Ah). If you meet one with the right item in your inventory, it gives the following speech:
"We sense... something... something ancient... a sickly smell... a chilling wind. My ancestors scream from within their chambers in my mind... but I cannot understand their words. This feeling... a memory? It sickens us, and for the first time in our lives... for the first time in generations... we fear."
To clarify, said inventory item is a Dnyarri, one of the psychic aliens who enslaved the Ur-Quan in ages past. As a whole the entire race was so evil that the Chmmr claims that if there was ever a devil, it was the Dnyarri.
Alex Mercer of Prototype may be a shapeshifting man-eating Humanoid Abomination and the stuff of New York's nightmares, but even he is shocked and disturbed by the sight of Elizabeth Greene's gigantic One-Winged Angel form, composed entirely of human flesh, crashing upward through the middle of Times Square and killing everything in sight.
Let's not forget The Reveal. The one responsible for the outbreak was the original Alex Mercer, the current Alex Mercer was an amalgamation of The Virus, the original Mercer in his death throes, and lots of other victims. After learning the reason why the original Mercer did what he did (out of spite), apparently The Virus was disgusted.
The Malkavian from Vampire: The Masquerade - Bloodlines is scared witless by the Cabbie and deeply disturbed by Mr. Ox. Exactly what these two characters are is unknown, but they've managed to unnerve a vampire is able to laugh off just about everything else the game throws at you and probably are nothing good.
By the Leviathan DLC for Mass Effect 3, Commander Shepard is the only thing the Reapers can really be said to fear. Bear in mind that the Reapers are a billion-year-old unstoppable force of hundreds or thousands of Eldritch Abominations that can, in many cases, throw down with entire fleets by themselves or in small numbers. And even though they're winning, they are afraid of you, although this generally manifests as them dropping all other efforts in order to attempt to laser you to death.
Early in Baldur's Gate 2: Throne of Bhaal the PCs stumble upon a vampire ring. Vampires, for most of the base game, have been tough opponents. However, at this point in the saga the party is supposed to be so beefed up, they do what they can to avoid the PCs. They still face the party though.
User Friendly has strips about Cthulhu being scared/bothered/worried/amazed about mundane things such as the RIAA's tactics, finance and accounting, etc.
Apparently at one point in the past Old Heterodynes meddled with the time itself, but while doing this they discovered something that terrified even them, the worst Spark overlords the whole continent trembled before. They turned their back on all the power they could possibly gain, because of this.
Similarly, another episode has That Guy describing something so horrific that SATAN HIMSELF is disturbed enough to censor him. This occurs twice in said episode.
In the occult/supernatural/monster community of the Global Guardians PBEM Universe, Nicholas Chandler is the most feared "mortal" on the planet, and merely mentioning Chandler's name to a vampire or werewolf tends to generate a flinch similar to what happens when a wizard hears the name "Voldemort" in the Harry Potter universe. What makes Chandler reallyBadass is that he's only fourteen years old. He's considered the "creepy little kid" in his neighborhood, and is distrusted by parents and children alike... until the children come to him telling stories of strange things bumping around their windows at night. At age eight he used a baseball bat to kill a menacing spirit, and he's succeeded in taking down every ghost, ghoulie, or monster he's come up against ever since.
SCP Foundation: The Foundation's attempts to pit living SCPs against SCP-682 in a bid to destroy it usually leave 682 alive but injured and the other SCP utterly terrified of 682. SCP-173 is noteworthy because it is the only thing that 682 fears.
Bugs Bunny short Hair Raising Hare. Bugs tells the monster who's been pursuing him that he's being watched by the audience. The monster says "People!", screams, and turns and runs through a series of walls. Watch it here.
The Classic Disney ShortLonesome Ghosts: Ghosts call Mickey, Donald and Goofy (who are ghost exterminators) and spend the rest of the cartoon scaring them. Then the three fall in the basement and end up covered in molasses and flour. The ghosts take one look at them, scream "Ghosts!" and run away.
In the Wacky Races episode "Creepy Trip to Lemon Twist", Dastardly lures the other racers into a Ghost Town, where he plans to scare them by dressing as a Bedsheet Ghost. It turns out that the town really is haunted, and its resident ghosts send several of the racers running away screaming. It might have gone on working, if they hadn't tried to scare the Gruesome Twosome and their dragon.
A Monster Clown featured as the villain on an episode of Ben 10's first series. Ben shows him what's underneath Ghostfreak's cowl, and he explodes.
Wakfu pretty much has a Benny Hill Show sketch of this trope where the girls are being chased by some monster, only for that monster and the girls to be fleeing from another bigger monster, and so on for about five different monsters.