Blood+: Diva is this to the Red Shield to the extent that, when directly confronted by her in Episode 24, Lewis is so thoroughly intimidated that he falls back on his ass, and is extremely relieved that she is more concerned with fighting Saya than eating him.
In Naruto, Orochimaru has this effect on people, freaking out even the likes of Ibiki Morino.
Pain. Jiraiya nearly shat himself when he heard that Pain had defeated Hanzo,who a younger Jiraiya had failed to defeat even with the support of his team. He goes to his Super Mode to counter Pain's power but sadly it's not enough, as he didn't have enough information on it. Sometime later Pain makes the whole of Konoha wet their pants when he effortlessly destroys the village.
Madara remains such a boogeyman that even decades after his death, the possibility that he might still be alive is enough to unite the entire Ninja World, which had been at odds with one another for generations, together to fight him.
Let's not forget Minato Namikaze, the Fourth Hokage and Naruto's dad. Nicknamed "The Yellow Flash," he was so feared by his enemies during the third war that a flee-on-sight order was issued the very second he appeared on the battlefield.
The Tailed-Beasts only fear one thing — the revival of the Ten-Tails, and for good reason. It is literally God of the Naruto World, and its mere existence caused complete and utter devastation. In fact, the Sage of the Six Paths, its Jinchuriki and the strongest shinobi to have ever existed, the founder of ninjutsu himself, feared that its revival would cause The End of the World as We Know It. Kurama's description of its power tells just how dangerous the Ten-Tails is.
Hanzo is insanely feared. How feared, you ask? So feared that the reason The Sannin are revered worldwide is because they fought him and survived. They didn't win, mind you - they fought him to a draw, and that alone is worthy of the title "legendary". It should also be noted that he wasn't as powerful as he used to be when Pein killed him.
Princess Kaguya, the first chakra user, and, according to her son, the Sage of the Six Paths, the most powerful person to have ever lived. She was initially worshipped as a goddess for ending all wars, but the violent tactics she used in order to keep the peace during her time made her feared as a demoness. When Madara transforms into her in Chapter 679 after being (literally) backstabbed by Black Zetsu, Naruto and Sasuke have major Oh Crap faces, indicating just how screwed Team 7 is.
Also, Barry the Chopper used to be this. Scar too.
King Bradley is so renowned for his sheer battle talent and commanding presence that near the end of the story, after the heroes already think they've won, the mere fact that Bradley steps up and announces "I'll take care of this" completely turns the situation around.
Izaya Orihara himself is somewhat of a lesser example, seeing as the only people who are really at risk are those he deals with most of the time, usually gangs. All the gangs are perfectly aware that pissing off Izaya is a stupid idea; as an Information Broker of the highest caliber, Izaya can screw you over the worst way possible at any time he so wishes. Attacking him is no good either, as Izaya is also famed as one of the strongest men in Ikebukuro (despite technically residing in Shinjuku), and one of the two people capable of fighting Shizuo Heiwajima without suffering grievous bodily harm. The fact that he regularly pisses off Shizuo for kicks should be an indicator of how dangerous he is.
Even the nastiest vampires and monsters in Hellsing are terrified of FatherAlexander Anderson. While Alucard isn't quite as well-known in the beginning of the series due to his years as a Sealed Badass in a Can, Anderson has an infamous reputation both among monster-hunting organizations like Hellsing and the bloodthirsty creatures that he enjoys filleting at every turn. He essentially functions as The Juggernaut for Iscariot and doesn't hesitate to destroy anyone or thing that gets on the wrong side of the Vatican or his moral beliefs. In the OVA, Integra even uses this to her advantage on two occasions, manipulating Anderson's strict moral code to utterly terrify and destroy a large chunk of the Nazi vampires while also convincing him and his subordinates to escort her home through hostile territory.
He also takes I Have Many Names to a whole new level. Paladin Anderson. Executioner Anderson. Bayonet Anderson. Angel Dust Anderson. Dust To Dust Anderson. Off With Its Head Anderson. Assassin Anderson. Regenerator Anderson. Killing Judge Anderson. Judas Priest. Monster of God. Iscariot's Trump Card. And those are just the names given in the main series.
Great Demon King Chestra, the Big Bad of Violinist of Hameln manga, inspires this reaction both through his reputation and his magical power. The entire armies are literally frozen in terror by his mere presence, implacably courageous characters doubt aloud whether they have a slightest chance against him, and greatest heroes of humanity see him in nightmares even after he is defeated.
Erza Scarlet in Fairy Tail is a rare heroic example. The entire guild freaks when it's announced she's returned from a mission, and nobody dares step out of line when she's around. Even Natsu and Gray stop bickering and pretend to be best friends.
Black Mage Zeref to the Magic Council. The mere mention of his possible return is enough to convince the first Magic Council to authorize a Kill Sat strike.
Acnologia the Black Dragon of the Apocalypse. Representatives from the second council immediately flee Tenrou Island when they hear Zeref mention Acnologia and when he appears the whole Fairy Tail pulls a Mass "Oh, Crap!".
Dragon Ball Z: Frieza and Majin Buu. Even the gods are terrified of them. When King Kai finds out that Frieza is also searching for Namek's Dragon Balls, he basically tells Goku to grab the Dragon Balls and run for his life, because if Frieza finds out he will hunt him down and kill everyone on Earth. Buu managed to kill all but one of the Supreme Kais and is fully capable of destroying the universe. Guess what he tries to do after turning into Super Buu.
For Vegeta it was the GinyuForce. Just hearing that they would soon arrive on Namek made him willing to team up with Gohan and Krillin.
Broly, in his first movie. Vegeta goes into a near-vegetative state after learning that he's the Legendary Super Saiyan.
Beers, in Battle Of Gods. Again, Vegeta is terrified of him, as are the Kais, and pretty much everyone else who knows who he is, including Shenlong!
Vegeta qualified in the Namek arc before the aforementioned Enemy Mine. None of the heroes were in his league until Goku arrived, he was actively searching for the same thing they were, and he was the kind of guy who would kill an entire village just because.
The Saiyans at the start of DBZ were the dreaded after it took Goku and Piccolo teaming up to just beat Raditz, who was far weaker than the two Saiyans coming to Earth. To further emphasis how outclass the fighters of Earth were, Goku had to sacrifice himself to win against his brother.
In the alternative timeline, the androids, specially 17 and 18.
King Piccolo was the original dreaded of the series. Everyone who knew him were terrified and Master Roshi, one of the biggest badass at the time, absolutely refused to even consider fighting him.
Goku was this to the Red Ribbon Army. He inspired fear in all the soldiers and the commanders, except for General Blue. When he came to the Red Ribbon base to take their dragon balls you can see the collective Oh Crap from everyone.
Yuu from Holyland wants to become this so that the bullies and gangsters will stop making trouble for him. It not working is a recurring theme of the series.
Zebra from Toriko. The entire world panics when he is released from prison. Just news of his release causes massive economic and social upheaval. And he hasn't even done anything yet.
What he DID do to get him into prison was Cause the extinction of 26 SPECIES. Said species were damaging the ecosystem, but still!
The Four Beasts — four vicious Gourmet World creatures that prey exclusively on humans — are so terrifying that news of their return causes a panic that dwarfs the upheaval caused by Zebra's release.
Joa the Dark Chef. Even Setsuna is afraid of this monster of a chef!
Accelerator in Index has this effect as well, just his arrival can scare the hell out of anyone who might have pissed him off.
Touma also has this effect to the magic side, to the point many magical organizations start sending assassins after him. All fail. The Kihara's of the science side may also have this reaction to him.
The Wretched Egg (a.k.a. the 'Red Man') in Deadman Wonderland is probablythe reason guards in the prison might actually have a lower survival rate than Red Shirts. There's a collective panic every time the Mother Goose System shuts off for any reason, and about the best you can hope for when crossing the Red Man's path is the opinion that you're more fun alive than dead, as was the case with Ganta and Hagire Rinichiro. So, of course, you can imagine Ganta's shock when he finds out that the same person who massacred his entire classroom, killed his best friend, gave him his Branch of Sin, and was responsible for everything in his life sucking was actually his childhood friend Shiro's Superpowered Evil Side, born from hellish, torturous experiments performed on her to unlock her full powers, and its awakening and subsequent gory slaughter of the scientists who experimented on her traumatized Ganta so much that he made himself forget Shiro even existed.
Johan Liebert is this in Monster, and FOR GOOD REASON!!! Anyone who has any knowledge of him (who's still alive that is) will generally begin to shake uncontrollably even thinking about him.
A psychopathic serial killer even kills himself when he's shown a picture of him.
When Anna, his own flesh and blood, confronts him with the intent on killing him, she falls to pieces as soon as he says hello and tries to kill herself.
In Rurouni Kenshin this is a common reaction to finding out the title character was once the legendary Hitokiri Battousai (this title, by the way, translates loosely as "Slays Men Just by Drawing His Sword").
Char Aznable, for the Federation. Witness the sheer panic that ensues in the original series whenever a red mobile suit shows up among the attacking forces.
Such is Char's reputation that any sight of a red mobile suit (save mass production types like the Marasai and the Rick Dias) will cause people to automatically assume Char's the pilot. As a side note, one of the more comical side effects of this pertains to fellow Zeon ace Johnny Ridden; as Johnny also pilots red mobile suits (such that his ace nickname is the "Crimson Lightning"), he's pretty much forced to live under Char's shadow (much to Johnny's detriment) as Federation pilots can't tell the difference between their machinesnote Johnny's MS tend to be painted in a crimson red with black trim, whereas Char's are either straight red or have accompanying pink...er, salmon trim.
After Char's Counterattack, the Federation was so afraid of Char possibly returning from the dead that Neo Zeon created Full Frontal, a Cyber Newtype modeled after Char's likeness and artificially indued with Char's memories, which were salvaged from the Sazabi's remains. While it was never made publicly clear in universe whether Full Frontal was Char or not, his presence was enough that he was dubbed the Second Coming of the Red Comet, and the Federation feared him as much as they feared the original.
Amuro Ray (the original Gundam pilot) was equally feared by both the Federation and Zeon remnants, if only for his raw Newtype powers and combat prowess; generally, whereas red mobile suits were automatically assumed to be piloted by Char, Gundams were automatically assumed to be piloted by Amuro (for a time anyway). In fact, the Federation was so afraid of the mere possibility of Amuro turning against them that they placed him under permanent house arrest in Wyoming; naturally, this did nothing to keep Amuro from escaping and joining the Karaba later on.
Kira Yamato has this reputation in Mobile Suit Gundam Seed Destiny. Very few people actually know his identity, but whenever "the Freedom" appears on the battlefield, expect a Mass "Oh, Crap!" He's even more feared because his ideology makes him a Wild Card from the rest of the world's perspective: he's a scarily good pilot in a superpowered mobile suit that seems to attack both sides indiscriminately, with most unaware of his true motives.
The three Admirals of One Piece are this for most pirates. Only the strongest of pirates don't immediately run screaming at the mere sight of an Admiral. And with good reason, considering all seen so far qualify as a Person of Mass Destruction: Aokiji is An Ice Person and can freeze oceans, tsunamis, and enormous sea monsters solid within a few seconds, Kizaru can move at light speed and launch Frickin' Laser Beams capable of effortlessly leveling trees the size of buildings, Akainu is a Magma Man, with a Devil Fruit that turned him into a freaking walking volcano. And the newest admiral, Fujitora, does not disappoint the admiral legacy: he has a devil fruit that controls gravity, which allows him to throw meteors at his enemies.
Admiral Akainu in particular stands out, as, on top of his formidable powers, he has a few doses of batshitinsanity. He stops at nothing in his quest to kill every single pirate in the world, and will gladly incinerate fellow marines if they object.
Other high-ranking marines with a sufficient reputation can also become this, such as Vice-Admiral Smoker.
Comedically, Vice-Admiral Monkey D. Garp is understandably feared by many a pirate due to the fact that he cornered the Pirate King Gold Roger numerous times when the man was still alive. Garp is also feared by his grandchildren though, but not because of his reputation. It's because of the Training from Hell he subjected them to during their Hilariously Abusive Childhood. Due to this, the only person that genuinely scares Luffy is Garp.
Whitebeard’s sole declaration of ownership of an island is enough to keep it out of harm’s ways and people with his mark on their back are deemed untouchable, because he is famed for going on Roaring Rampage of Revenge against anyone, who has laid even one finger on his crewmen. Many characters have an Oh Crap moment, when they hear that the World Government decided to publicly execute Portgas D. Ace, which means an open declaration of war against the World's Strongest Man.
To clarify, Whitebeard is THE The Dreaded and for good damn reason. World's Strongest Man you say? This guy so deserves this title that the World Government busts out their entire military might, including all three Admirals, just so that they even have a smidgeon of hope of actually competing in a battle, let alone a prolonged war against this guy. Coming from an elderly man in his seventies, far out of his prime, and to top it off is in the advanced stages of a terminal illness and during any of his fights, has to take breathers because his heart's giving out on him!!!! He's pretty much this world's version of Chuck Norris until his death.
Silvers Rayleigh, Roger's former second-in-command, is similarly terrifying. When Garp (the man who captured Roger, mind you) received word that he was in the area, he ordered his men to not engage him and to keep hush-hush about it with Sengoku, with the reasoning being that the prospect of dealing with Whitebeard was terrifying enough, and that having to deal with him AND Rayleigh was simply not something that they could even hope to manage. Sure enough, when Rayleigh finally does come into contact with Admiral Kizaru, he not only manages to fight evenly with him, but actually WOUNDS, despite him being a Logia, even as he admits that he hasn't seen combat in over twenty years and is a tad rusty.
Other pirates of sufficient power can be this trope. The people of Fishman Island become terrified when they realize how close they are to experiencing the wrath of someone on Whitebeard's level of power. The marines of G-5 (a Marine branch full of jerkasses that love to torture pirates and refuse to obey headquarters) panic at seeing Trafalgar Law, a member of the Shichibukai who sent the Government a hundred hearts to join. Back in the East Blue, people are scared of the idea of pirates like Krieg and Arlong coming.
In fact, Luffy himself (and by extension, his crew), have already hit this status, especially if you account in his bounty. He would be feared in every sea in the world except the New World, and even then he's already made an impression there.
Case and Point: Luffy's at Corrida Colosseum for a Tournament Arc while wearing a ridiculous Paper-Thin Disguise that manages to fool everybody. There, while speaking with one of the other competitors, Luffy (being Luffy), forgets that he's incognito and proceeds to give out his real name. Everybody immediately freaks out, and only calm down when they see the sign on the back of his shirt say 'Lucy,' along with remembering rumors about him being an eight-meter tall giant. Luffy's become so infamous that literally anybody who isn't at the strength level of the Shichibukai (who are notable New World veterans) instantly fears him.
Strangely, out of all of the current members of the Yonkou, the one that stands out the most as this trope is the one who hasn't made an official appearance in the manga yet: Kaidou. He managed to scare the hell out of Donflamingo, to the point that the man willingly stepped down from his position as a Shichibukai rather than facing him, despite the fact that it would force the World Government to have him hunted down by the Admirals. When you make the aforementioned Admirals look like the friendlier option, you are this trope Up to Eleven.
Don't forget about Luffy's father, Dragon. He hasn't done much of anything in the series proper yet and he's still known as the "World's Most Wanted Criminal." He's considered a threat equal to Whitebeardwhen Whitebeard was still alive, perhaps even more of a threat due to the fact that he's far more active.
It also applies to those subordinate to him with significant power to warrant a threat. For example, his second-in-command, Sabo, who was enough to freak out nearly every single person on Dressrosa once they realized who he was, barring Fujitora and Doflamingo.
The Shichibukai rely on this to instill fear in other pirates. Despite being derided as "government dogs," they are nonetheless insanely powerful and feared, and their reputation is what the World Government relies on to help keep the pirate population down. Pissing one of them off could be as bad as pissing off one of the Yonkou, depending on which one.
The Eleven Supernovas are feared due to their willingness to challenge the Yonkou and the status quo and for their chaotic nature, along with their potential. When they first entered the New World, they caused so much chaos and destruction that they got lumped with the moniker "The Worst Generation." The reputations of both Luffy and Law show just how much of an impact they've made.
Seimei of Loveless is definitely the most feared of the series. Usually used with a pretty little topping of Oh Crap. What makes him even more creepy is that just about this entire trope applies to him. The Fearless Fool does indeed cry in fear, and The Pollyanna does indeed despair over The Stoic being defeated, who also lost his cool. In fact, his appearance alone isn't the only way he causes genuine fear - he uses words to, effectively, freak. People. Out.
Guts from Berserk is this when he was known as the Hundred-Man Slayer before the Eclipse, and post-Eclipse when he is now known as The Black Swordsman.
Nosferatu Zodd is well-respected/feared by mercenaries as the "god of the battlefield". And they don't even know that he's a powerful demonic Apostle.
By the second half of Death Note, Kira has become such a terrifying entity that merely the presence of Kira has changed the world on a global scale. Crime rates have dropped significantly, simply out of the fear of being murdered by a judge outside of the legal system. When Near corners Light at the end of the series, he even notes that he's not the judge of good and evil, and that Kira may have changed the world for the better with fear.
During the final arc of Eyeshield 21, Donald "Mr. Don" Obermann of the American Pentagram takes on this role. A seven-foot Genius Bruiser and Juggernaut, Mr. Don plows through the cream of the Japanese team as if they were so many bowling pins, a fact that leaves most of the other characters shaking. He terrifies Sena, Monta, and the rest of the Deimon players, manages to put the fear of God into Agon, and leaves everyone with the impression that he cannot be stopped; the only one who doesn't fear him is Gaou. During the Kantou Regionals Arc, Agon and Gaou themselves had this status, terrifying both opposing players and their own teammates.
Slayers has Lina Inverse nicknamed "the Dragon-Spooker" and "the Bandit-Killer". Pretty justified, considering the trail of destruction she leaves behind her and her questionable motivations.
The one whose presence does disconcert the dragons visibly is Xellos, though — after the carnage they suffered from him in their last war. He even used this status, though only to cut short their tendency to muck around and get things dragon themselves could see as desirable eventually done right now. He also seem to perceive Filia's meandering between haughty disregard and sheer horror as either amusing or refreshing.
After the events of Volume 12 in High School D×D, the protagonist Issei becomes this in the eyes of the Anti-Lord of Hell faction. The reason being that they've tried all sorts of possibilities of killing the current Red Dragon Emperor to the point that they had to resort using Samael, the dragon eater, and he still lived through that made them fear him.
Parodied at Muteki Kanban Musume: To hear Kayahara sensei’s name is enough for the students of her school to scream and run in panic... she tries to be a Save Our Students teacher, but she is so depressed, she constanstly spoofs Sadako Yamamura, stringy hair and all.
In Bleach, this was originally played for laughs with Retsu Unohana, captain of the 4th Division. Then it's revealed she was the original Kenpachi, Yachiru Unohana. She has mastered every sword style and was the worst criminal in Soul Society history (even Aizen doesn't have that reputation).
Beelzebub has loads and loads of people who fill this role. Fist we have "Devil" Oga Tatsumi who in his opening scene is shown to be making local delinquents fear him. As the manga progresses only the suicidal, stupid or people who are using the powers of demons (or high ranking demons themselves) don't run from him in terror. It becomes an almost running gag with thugs giving him grief only to realize who they're dealing with and turn to jelly.
Each of the 4 members of the Tohoshinki (especially Tojou) to the point that a school that has been imitating them craps themselves when they realize they're dealing with the real Tohoshinki and not another group of imposters. Their counterparts the Rokkisei (6 Knights) also count (especially their head Izuma who makes his subordinates crap their pants)
Jabberwock and Behemoth. Behemoth makes Satome, Isugugi and Ittosai Kunieda (the previous generations of bad ass) nervous and even he can't control Jabberwock. Of course none of this stops Oga from beating him half to death
The Colossal Titan and Armored Titan from Attack on Titan, and for good reason. Their appearance brought a century of peace and safety to an end, and resulted in the loss of 20% of the human population. Humanity lives in constant fear of them, aware that should they make another appearance there will be almost nothing the military can do to stop them. Extinction of the human race is a very real possibility, and everyone knows it.
Levi, with being the World's Strongest Man. If even the Female Titan aka Annie was terrified of him after he tells the latter he wanted revenge, then so should you.
Reaching levels past even those three is the mysterious Beast Titan. He's enormous, only second in height to the Wall sized Colossal Titan. He's intelligent and capable of speech and strategy, leading Titans in coordinated assaults on humanity. And he can turn people into Titans through some unknown force. The heroes acknowledge he's probably the biggest threat in the series.
Afro from Afro Samurai. The Number Two Headband, and the right to challenge the Number One, the equivalent of God in the setting, has traded hands many time, but only the Afro Samurai is the one who has kept it the longest, to the point people are alarmed such a person actually exists. Best exemplified in the extended version of episode one, where half the audience are foolhardy Mooks thinking they can grab the prize, and the other half recognize they are in the presence of a "demon" travelling to kill God himself.
Jotaro Kujo from JoJo's Bizarre Adventure grows up and becomes one after his debut in Part 3. When he reappears in Parts 4 and 6, he's gained a reputation among other Stand Users not only for the raw power of Star Platinum, but also his high intelligence and great deductive powers, letting him coolly track down his enemies and dismantle their plans before they even begin.
Mikan from Rising X Rydeen, also known as the "lightning god". Most of the bad guys are aware of her reputation and are smart enough to try to run away from her but she can move as fast as lightning so they're usually forced to fight her anyway.