When your name sounds like "Saccharine", people probably expect you to be as sweet as your name, right? Not true for the Big Bad in The Adventures of Tintin, where Mr. Ivan Ivanovich Sahkrine is willing to kidnap, murder, and steal all to find the location of Red Rackham's Treasure. Well, he is Rackham's descendant and possible reincarnation, after all.... note However, it should be noted that it is a case of Adaptational Villainy; in the original graphic novel by Hergé, Saccharine (written Saccharine, not Sahkrine) was actually a friendly Red Herring.
Coco: Mamá Imelda has an alebrije, a powerful spirit guide that takes the form of a multicolored winged jaguar. Its name is... Pepita ("pumpkin seed"). In life, Pepita was a housecat.
In Frozen, the Snowlem bodyguard Elsa conjures in one last desperate bid to convince her sister to leave her alone is nicknamed "Marshmallow" by the happy-go-lucky snowman Olaf. At first it appears to be a one-off joke, but this persists through the credits, into all auxiliary material, all the way to his appearance as a Guest-Star Party Member in Kingdom Hearts III.
The main villain of Heavy Metal 2000 is given the terror-inducing name of... Tyler. This is because he wasn't evil to begin with, only becoming an Ax-Crazy warlord after being exposed to the Loc-Nar.
How to Train Your Dragon: Toothless is a member of the most feared species of dragon that is known to the Vikings, though he doesn't get the name until after he's been at least partially domesticated. His teeth are retractable.
Lilo's social worker in Lilo & Stitch is a huge black man (voiced by Ving Rhames in the movie, no less) who habitually dresses in formalwear and a gold earring... named Mr. Bubbles. Subverted in that his first name is Cobra.
The Bowler Hat Guy's Hypercompetent Sidekick and partner in crime is a robotic bowler hat named Doris. She turns out to be the real mastermind, taking over in the Bad Future Bowler Hat Guy unwittingly helped her create. Her name is adopted from her designation, DOR-15.
At one point, Bowler Hat Guy sics a brainwashed Tyrannosaurus rex named "Tiny" on Lewis.
I've got a big head, and little arms. I'm just not sure how well this plan was thought through... Master?
Over the Hedge gives an in-universe example. The animals are utterly terrified of the titular hedge when it's first encountered. How do they defuse the tension?
Hammy: Lets call it Steve. [Vern looks at Hammy questioningly] Hammy: It's a pretty name. Other animals: Yeah, I'm a lot less scared of "Steve".
Fluffy is a 1965 Tony Randall film about the title character, a full grown household dwelling lion.
In Kung Pow! Enter the Fist, the main (male) villain was named "Betty". It's actually quite a bit worse than that, his name used to be "Master Pain;" he then changed it to Betty.
In Winter's Bone the criminal, prone-to-Ax-Crazy-violence, meth-addicted uncle of the main character is named... "Teardrop".
Double example: The name used by the Devil in The Exorcist AND by a psychotic killer in Strangeland? Captain Howdy.
The diabolical crime lord from RoboCop (1987) has the unassuming name of Clarence. In keeping with the joke, he also looks like a balding, bespectacled accountant (the director went with this look because he wanted a villain evocative of Heinrich Himmler).
Diamonds Are Forever: Two of Blofeld's minions who are keeping Willard Whyte prisoner in his house are named Bambi and Thumper. They prove to be a little difficult for Bond to deal with.
'Pumpkin'/'Ringo' from Pulp Fiction isn't psycho enough, but his girlfriend 'Honeybunny' most definitely is.
Metropolis: Dr. Rotwang. It sounds like some kind of horrible disease in English, but "Rotwang" is actually German for "red cheek".
Not a creature but it still fits the trope: the gun that Kay gives Jay in Men in Black is a tiny little thing that looks rather like a water pistol. It's called a Noisy Cricket. And when Jay fires it the first time, it takes out a wall, and the kickback is enough to throw him back several metres.
In Trick 'r Treat, the monstrous king of Halloween is named Sam. Short for Samhain.
In the Katharine Hepburn/Cary Grant screwball comedy Bringing Up Baby, "Baby" is a fully-grown leopard. He's friendly enough, but he's still a leopard.
In Seven Samurai, Toshiro Mifune's character is named Kikuchiyo after the fake papers he has to "prove" he's of noble birth. Unbeknown to him and to the amusement of the others, Kikuchiyo is the name of a little girl. He still kicks lots of ass.
In The Unborn, the spirit of the unborn child terrorizing Odette Yustman's character is named Jumby.
Bunny in Platoon, a soldier who rapes and kills civilians during a pacification mission in a Vietnamese village.
The Jungle Book (2016): The King of the Bandar-Log monkeys is a 12-foot tall hulking Gigantopithecus who talks like a mob boss. His name is Louie. This is a result of the film making him an Adaptational Badass. In the source material, Louie (originally an Orangutan) was not an intimidating or villainous character, so the name was more fitting.
The titular monster from The Bye Bye Man drives people into hallucinatory insanity that causes them to commit hideous acts of murder just by thinking of his name.
Captain Marvel (2019): Every alien who meets Goose treats the cat as a scary dangerous creature. They're right.
In Act of Vengeance, the police have nicknamed the serial rapist "Jingle Bells", because he makes his victims sing that song as he rapes them.