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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.
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.
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.
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.
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.
Princess Azula from Avatar: The Last Airbender. Being a Machiavellian tactical genius, she deliberately goes out of her way to solidify this image of herself, believing in 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.
In The Legend of Korra, 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 season two, Vaatu. 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.
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.