Jafar, the villain of Aladdin, was actually given a snake motif: his hat and robes resemble the hood and body of a cobra, he has vaguely serpentine eyes, teeth resembling a venomous snake's fangs, a constant tendency to flick out his tongue while speaking, he always carries a cobra-headed staff with him all the time, and at the end of the film, he eventurns into one.
Manolo with bulls. He comes from a family of bullfighters, but can't bring himself to deliver the final blow.
Joaquin with eagles, given the small, but generous number of them surrounding him throughout the movie.
Xibalba with snakes, given his magical staff is a two headed snake. Word of God even states that the snake staff is actually a part of Xibalba himself.
From Coraline, the Other Mother is especially given imagery of a spider. It's revealed to be her real form, and her kind is known to eat their offspring.
Bugs are everywhere in the film as well. The Other Mother added them to the Other World because she thought Coraline liked bugs.
An in-universe example in Brother Bear; the protagonist's spirit animal - much to his annoyance - is a bear, and he ends up getting transformed into one.
Kung Fu Panda takes it so far as to name characters after what species they are (or what style of kung fu they practice). For example, Tigress practices Tiger Style, and her personality is deeply emotional and fiercely competitive. Monkey is playful and used to be the town prankster.
Crows appear frequently in Loving Vincent as Armand's mission shifts from finding a recipient for Van Gogh's undelivered letter to working out how and why he died. The painting Wheatfield with Crows forms the basis for several scenes.
Many of the characters in Blade Runner are associated with an animal, including all of the (confirmed) Replicants. Roy Batty, in fact, has two.
Bram Stoker's Dracula has the obvious bat, rat and wolf associations for the titular character, but there's also a snake motif for Lucy: her first appearance has her wearing an evening gown with snake embroidering and a hairdo resembling coiled snakes, the nightgown she wears when attacked by Dracula resembles a snake's belly, and her wedding/funeral dress was inspired by frill-necked lizards.
In The Dark Knight, the Joker makes some references about dogs and their loyalty. One of the gangs in Gotham is led by a man who starves and abuses a group of dogs to make them viciously attack anyone. Joker sets them on him.
The last shot of The Departed, a movie about a pair of moles within the Boston Mob and the Mass. "Staties" hunting each other, features a rat scurrying across a balcony
Spoofed on The Simpsons which did a parody of this movie. As the rat scurries by at the end, Ralph pops up and tells the audience, "The rat represents obviousness!"
In Ever After, when preparing for the masque, Marguerite is dressed as a peacock, beautiful and vain. By comparison, her sister, Jacqueline, who is kind and sweet, is dressed as a horse. The brief conversation they had before leaving also reflected Jacqueline's situation. She complained that she always wanted to be the peacock (someone beautiful and admired like her sister), in which her mother then told her a horse is still a noble creature. In the end, she chooses to help Danielle and falls in love with the guard captain, living happily in the castle with her stepsister, unlike her mother and sister.
Psycho also has a bird motif, associating Norman Bates' female victims with the birds he stuffs. He comments that Marion Crane (note the surname), from Phoenix, Arizona, eats like a bird shortly before killing her. In the finale we learn that he has preserved the corpse of his mother with his taxidermy skills. There are many, many different references to the bird motif throughout the film. Try to find them all!
In Rebecca, the animal favoured by the nameless heroine is the lap-dog, Jasper. Rebecca, however, is regularly mentioned in conjunction with horses. The second Mrs. de Winter is meek, mild, and childish, always eager to please and desperate for her husband's approval, to the point where she is almost pathetic. Rebecca, however, is wild and dangerous and too powerful for Max De Winter to keep control of - especially since the horses mentioned alongside her are crazy with pain, as Rebecca whips them into a frenzy.
From Sherlock Holmes (2009), a crow is always seen whenever Lord Blackwood is about to kill someone. So at the end, when Lord Blackwood really does die for real, it flies away. The crow turns out to be nothing more than a normal crow.
At one point in Star Trek (2009), McCoy indirectly referred to Kirk as a stallion, who had started out wild, reckless and proud. Eventually, he does grow up and becomes "tamed" and more controlled of his emotions.
The Wolverine: Next to the Wolverine, we also have the Viper, and the film alludes often to the animalistic natures of both.
In the opening credits of the 1939 film version of The Women, each major character is represented by an animal, which dissolves into the face of the actress. (As with the human characters, all animals in the movie were female.)
The Conspiracy: Members of the Tarsus Club are divided into ravens and lions, complete with masks, and the core of their mythos is the worship of Mithras with a heavy focus on the bull hunting-and-slaying scene and a ritualistic murder symbolic of the latter in every meeting.
Skyfall: Raul Silva compares himself and Bond being betrayed by the MI-6 and targeting each other; to rats who forced into a barrel, resorted to cannibalism, and even when released still choose to eat nothing but their own kind. Bond notes on this after he knifes Sliva in the back.
Franz Oberhauser describes Bond as a cuckoo because Bond was adopted into Oberhauser's family and his father loved Bond more than Oberhauser, likening it to how a cuckoo bird would lay its eggs in another bird's nest and kick out the original eggs.
In the 2016 The Great Wall, each of the five main groups of warriors protecting the titular wall are coded by the animals on their helmets and ornaments. The horse-riding cavalry are represented by a purple stag. The archers perched at the top are represented by a red bird. The artillery group handling the cannons and heavy-lifting are represented by a golden tiger. The elite female troops who spear their enemies from above are represented by a blue crane. And the main military force guarding the walls are represented by a grey bear.
In the 2016 film Before I Wake the child protagonist Cody is associated with butterflies due to his love of them. Whenever he falls asleep glowing butterflies are presented. In the final act Cody desperately protects social services by sticking them to the walls by the use of chrysalis. Jessie also defeats The Canker Man by presenting a butterfly pillow to it, in the end a smiling Cody learns to control his dreams by creating a dream butterfly in his open hand.