Aladdin: The Series: Destane, the previous ruler of the Land of the Black Sand before Mozenrath usurped him, was apparently so vicious and powerful that Jafar himself steered clear of him. Also, Genie is terrified of Mukhtar, and rightfully so, as they are a species whose very purpose is hunting and killing genies.
In The Transformers, natives of Cybertron are terrified of the Guardian Robots, titans who, as their name suggested, guarded large cities back before the Great War. In one episode, the Decepticons find an obviously dead one - its head is missing - and Rumble says that even the site of it gives him the creeps. This also applies to Omega Supreme, the last still functioning one; in another episode, Starscream trembles at the thought of making an attack against him.
Megatron is this in Transformers Animated. The Autobots regard him as a bogeyman who is reputed to eat protoforms - baby Transformers. The other Decepticons are viewed this way as well. The Autobot leaders are so afraid of them that Ultra Magnus and Sentinel Prime would rather deny the Decepticon presence on Earth than cause a panic among the populace.
Soundwave in Transformers Prime is this to the other Decepticons due to his role as communications chief, which helps him keep down insurrections. It's why Starscream goes out of his way to stay on Soundwave's good side — he knows full well that he can't take command of the Decepticon forces on Earth without Soundwave's approval.
Don't let his slow moving nature and silence fool you, Soundwave is fully capable of beating insubornates within an inch of their lives. Airachnid learned this first hand.
Bumblebee: "Two humans, a Mini-Con, a Dinobot and an Academy Cadet against Soundwave and Laserbeak? You realize that had about a four percent chance of working?"
General Grievous in Star Wars: Clone Wars. His near-victory against five (albeit exhausted) Jedi established him as a fearsome enemy. Count Dooku actually taught Grievous to use fear as a weapon, telling him that without it he wouldn't stand a chance against the best of the Jedi.
Zecora is this to the population of Ponyville at the start of "Bridle Gossip," who believe her to be an evil enchantress thanks to her strange mannerisms and residency in the dreaded EverfreeForest. She's revealed to be perfectly nice by the end of the episode.
King Sombra, the antagonist of the "Crystal Empire" two-parter. Simply thinking about his reign causes his former subjects to shudder; in fact, though he cursed the crystal ponies by wiping their memories, one of them implies that part of their amnesia may instead be due to their suppressing what little they do remember. When Twilight Sparkle has to find an ancient relic that Sombra hid away, she deduces (correctly) that he hid it somewhere in his own castle, because he was banking on everyone being too scared of him to ever search the place.
LordTirek from the season 4 finale, when first introduced, isn't overly dangerous, as he is decrepit and sickly, but what makes Tirek dreaded and dangerous is his Mana Drain ability. Tirek can steal the magic and talent from any ponies he comes across, rendering them completely helpless. It was bad enough that sending Discord after him was the first course of action taken. We eventually learn later just how dangerous he can become once he absorbs enough magic, by effortlessly draining Discord of his magic.
Breach from Generator Rex becomes this in "Lions and Lambs". Everyone who knows what Breach can do fears her. When Six notices the Providence troops are trembling, he asks Rex if they have any experience with Breach. Rex says that's the problem, shuddering as he remembers what Breach did to him.
Almost every member of the Kids Next Door is terrified of Numbuh 86, and not just because she has a foul temper; she has the authority to have them decommissioned. (That's her job.) Of course, she quickly becomes a Miles Gloriosus when faced with a problem she can't handle.
Azula from the original Avatar: The Last Airbender. Being a Machiavellian tactical genius, she deliberately goes out of her way to solidify this image of herself, believing in power and manipulation through fear and might. For much of the series, it works spectacularly, with even her Uncle Iroh showing fear of being in her clutches, and leading to her turning an entire Government Conspiracy group against their leader through sheer intimidation and force of personality alone. Unfortunately for her, it stops working when Mai's love for Zuko, and Ty Lee's friendship with Mai, become stronger than their fear of her.
Of course, even Azula cowers in the presence of her father, Fire Lord Ozai.
Amon, the leader of the Anti-bending Equalists, is this, thanks to a combination of his creepy masked appearance, his even creepier (and very competent) minions, and his ability to permanently remove a person's bending. Korra is terrified of him and sees him in her nightmares.
To say nothing of the Bigger Bad of the franchise, Vaatu, who becomes the Big Bad of the second season. Of course, he last showed up so many millennia ago that few actually know who he is. Once they do, though, it's pretty clear Korra's the only one who can do anything and the world can only stare and go Oh, Crap! at the final confrontation. Even his herald Unalaq fears his retribution if the Avatar isn't brought to him, and Varrick acknowledges Vaatu as the greatest evil of all existence.
Everyone takes Zaheer and his cronies very seriously, even characters who are quite badass themselves. Once Zaheer himself escapes, the leaders of the other nations immediately put everyone they can trust on the job of guarding the other three. Also, Tenzin's reluctance to let Korra go to Republic City at the beginning of the series (which means she'd been stuck on Air Temple Island until her late teens!) proves to be because of these guys. Everyone was so worried about protecting her from their conspiracy even though they'd been in Tailor Made Prisons for some time that she had to really fight for the right to get out and start Avatar-ing.
Kuvira, the Big Bad of Book 4. During the Time Skip between Books 3 and 4, she was tasked with restoring the Earth Kingdom and has quickly become someone to both respect and fear, earning the monkier of "The Great Uniter". This is most evident in the first episode where a group of bandits attack her train. One Curb-Stomp Battle later, they realize exactly whose train they tried to rob and they're pratically soiling themselves and begging for mercy. Bolin and Varrick later exploit this by threatening to report a guard to Kuvira if he didn't let them and a group of prisoners pass.
In Jimmy Two-Shoes, Lucius I-the original ruler of Miseryville-is this. He's never actually been shown on the show, but he was mentioned in one episode, and it was shown that all the rest of the Heinouses (all of whom are basically different incarnations of Satan) are horrified by him.
Ben10: in a universe filled with Eldritch Abominations, Evil Sorcerers, Alien Invaders with Death Rays available on a large scale, Ghost Aliens Evil Overlords, Monster Clowns and psychotic mutants amongst other things, Vilgax is still considered the most dangerous being. Known for having conquered ten worlds, five others and created a black hole, he was in fact so feared in the Original Series that no organic life form was willing to work for him, forcing him to use Mecha-Mooks as his personal army.
However, back on his home planet, he is actually a very beloved leader, and he has many Pet the Dog and Licked by the Dog moments; Ben was utterly flabbergasted by this. It's to the point that a newer villain attacks in force, he decided to try to take out Vilgax to demoralize his people. (Spoiler alert: Vilgy kicked the assassins' butts. Without any of his usual weaponry.)
Ma Vreedle. A heaping dose of crazy, mixed in with a deceptive streak of cunning and a mean punch. Nobody wants to mess with her. Even Vilgax is sent screaming off planet at the sight of her.
Total Drama All-Stars has Mal, one of Mike's personalities whom all the other personalities (Chester, Svetlana, Vito and Manitoba Smith), and Duncan fear. In "Evil Dread", as his other personalities talk about him returning after years of absence, Svetlana is clearly terrified and Vito worries about how they can stop him. Chris, Chef, and Alejandro are mortified of him as well.
In the original Bugs Bunny shorts, the Tasmanian Devil was this. Every single animal in the area would panic and clear out when he started approaching.
Yosemite Sam was this in many cartoons as well, especially in the Wild West settings.
According to Journal 3, the most dangerous creature in Gravity Falls is Bill Cipher, a demon that looks like the Eye of Providence with arms, legs, and a top hat. DO NOT SUMMON AT ALL COSTS!
Princess Fang, one of the protagonists of Dave the Barbarian, is known only as "the Great Destructor" to all bugs, ranging from small cockroaches to hordes of car-sized Blugelbeetles.
The Beast of Over the Garden Wall is treated as such by every character the brothers interact with who have even heard of him. Most notable in Chapter 4, where a very jovial party is turned into a tavern full of fear when Wirt mentions him.
Mandy of The Grim Adventures of Billy & Mandy. An odd example, in that how much people fear her seems to be directly rather than inversely correlated with how much of a danger she is to them. Irwin and Mindy, both of whom are non-Badass Normal human children with no powers, frequently and deliberately antagonize her without fear of consequence, and low-level monsters will often try to frighten her at first, but she'll usually scare them off, while Grim, the nigh-omnipotent, immortalpersonification of death, is terrified of her and will do anything she says.
The Family Guy episode "A Fistful of Meg" has Mike Pulaski, a psychopathic bully capable of killing anyone who slights him. It's said that he once knifed a kid on the playground (then beat up the knife) and that he can watch Friday Night Lights without crying.
Tina is this to the students and faculty of Elmore Junior High. Understandable, considering she's a Tyrannosaurus rex in a school where many students could be easily killed or maimed even by a normal human.
In Spliced, every mutant on Keepaway Island is utterly terrified of both the Wunny Sharbit and Mister Smarty Smarts. In the case of the Wunny Sharbit, it's fully justified, as it's a creature specifically and successfully designed to be the most dangerous animal on Earth. Mister Smarty Smarts' status as this is harder to understand, seeing as he's an Ineffectual Sympathetic Villain who is really more obnoxious than threatening.
In "The Return," Jasper mentions someone called "Yellow Diamond" in a throwaway line. At this point we know nothing about her, but it's telling that both Perdiot and Lapis Lazuli, who are apparently on her side, look scared just at the mention of her name.
Ironically, Pearl of all gems is this to the Homeworld gems back in the days of the War. She's described as a "terrifying renegade" and it shows when she effortlessly cuts down two warrior class gems in about as many seconds. This despite apparently being "someone's shiny toy" according to Peridot.
In Mike Tyson Mysteries, "Heavyweight Champion of the Moon", Mike gains a reputation for getting into "fender benders" with his vehicle, and has so far killed 10 people, specifically astronauts, including Buzz Aldrin. After Mike hits and kills his 11th up on the surface of the moon, his insurance representative realizes that Mike has actually only killed 2 astronauts, and the other 8 were astronomers. By this time, astronomers everywhere are already living in fear.
From Spongebob Squarepants, we have the ALASKAN BULL WORM(!), a borderline Kaiju which slithers along eating everything (and everyone) in its path. Everyone in Bikini Bottom is terrified of it, with even Mr. Krabs declaring that no one would ever be foolish enough to go after one. The only one who doesn't fear the thing is Sandy, who is primarily motivated by Hubris and revenge (it ate her tail) and had never actually seen the worm with her own eyes before. When she finally does, she runs for her life.
In Rugrats, nearly every kid except Susie and occasionally Kimi is afraid of Angelica. Even fearless leader Tommy Pickles finds her terrifying. Played for laughs sometimes, for example when she's hiding in the bushes at Tommy's house and everyone initially thinks she's a monster.
Angelica: (bursts out of the bushes with a big Cheshire Cat Grin) Chuckie: AHHH! IT'S WORSE THAN A MONSTER! IT'S ANGELICA!
In Fairly OddParents, Timmy becomes this to the Yugopotamians because to them, Good Is Bad And Bad Is Good. Acts like skipping across a fluffy carpet, eating chocolate, and hugging a teddy bear are forms of torture for them, so Timmy being able to do all of them in succession makes him some kind of Humanoid Abomination to them.
Gunmar the Black emerged from a corrupted Heartstone and terrorized so much of the world that it took whole armies just to barely do any damage, taking an exceptionally strong Trollhunter to banish him. Even the other Trollhunters in the void believe him to be unkillable.
Changelings are so feared and hated that word of it escaping to Trollmarket's public would have led to mass panic.
Bular is infamous for being Gunmar's son, and is considered a threat to all of Troll-kind.
Angor Rot was so powerful that it took all of Trollmarket to face him and his magic. Plus, he built a reputation for killing seasoned Trollhunters.
Bucky O'Hare and the Toad Wars: The toads are genetically pre-disposed to have a Bring My Brown Pants moment whenever they see a Betelgeusian Berserker Baboon. When that vulnerability is neutralized... the toads still crap themselves at the thought of actually having to fight Betelgeusian Berserker Baboons.
Air Marshal: Wait a minute! Now, the goggles are a neat trick, but the Betelgeusian Berserker Baboons are our most formidable foes in the Aniverse!
Just about everyone in Bump in the Night is afraid of the Closet Monster, an animate pile of dirty clothes that often tries to harm the main characters.
Samurai Jack: Aku, the Master of Masters, the Deliverer of Darkness, the Shogun of Sorrow... need we go on? He is a demon so feared that his return after the Emperor first defeated him would spell doom for the world. People know better than to cross him and elders often warn children to think twice before speaking ill of him. His followers often fear getting on his bad side when in his presence, as shown in "Jack and The Gangsters" when the titular gangsters report back to him and they think anyone who tries to fight him is out of their minds. Plus, when Aku appears before an audience of children in "Aku's Fairy Tales", they are absolutely terrified.