There was Mantis, a praying mantis, as the Pint Sized Powerhouse.
Po: Wow, you guys are The Furious Five! You're all just like your action figures, only bigger! Except for you, Mantis, you're about the same.
Shifu's not as tiny as Mantis, but he's considerably shorter than most of the cast. He takes on the Furious Five all at once in the beginning of the film (of course he trained them in the first place, which says a lot), beats up Po, and manages to hold off Tai Lung in the climax of the film.
In Wreck-It Ralph, Fix-it Felix Jr. qualifies as this. Although half Calhoun's height, he can lift her with one arm while holding onto a rope with the other.
Tangled: Rapunzel, who is able to lift Mother Gothel up and down the tower every day using her hair and her hands. She makes it look pretty much effortless. Also, she manages to knock Flynn Rider out several times with a frying pan, and later helps him escape some guards by letting him swing on her hair.
Frozen: Anna, who is able to sucker punch Prince Hans (who is several inches taller than her, and noticeably better built) into the fjord at the end of the film effortlessly. She is shown running around the castle Le Parkour style earlier, so she may be small in stature but incredibly strong, like a ballerina.
In the climax of The Book of Life, the small, thin Maria managed to flip-kick Chakal, a strong and muscular man.
In Big Hero 6, Hiro's bot that he uses for bot-fighting is small and toy-like, but easily beats a much larger bot because of its maneuverability and ability to disassemble/reassemble itself.
Ewoks. Cute little teddy bear-like aliens who can overpower combat trained humans in hand-to-hand combat with little effort. During the Battle Of Endor, some Ewoks can be seen throwing Stormtroopers around like ragdolls!
Princess Leia in the original trilogy and her mother Padme in the prequel trilog are played by 5'1" Carrie Fisher and 5'3" Natalie Portman, respectively, but they are both competent Action Girls who can hold a fight.
Shortness and ass-kicking combined seems to run in this family. According to The New Essential Guide to Characters, Luke Skywalker is only 5'6".
Rey stands 5'6'' too, according to her stats on Wookiepedia.
Emperor Palpatine by the time of Return of the Jedi is also 5'6", down from an original height of only 5'8". And he's still the most powerful, terrifying Sith Lord of all time.
Rogue One also features a vehicular version in the form of the Hammerhead corvette, a Rebel ship a fraction of the size of a Star Destroyer but with an armored bow and engines powerful enough to ram a disabled destroyer through a second one and into the shield gate, destroying all three Imperial ships.
Mini-Me in Austin Powers. He's officially one-eighth Dr. Evil's size, and can take on Austin in a one-on-one fight. He's also a sneaky little guy.
The Chronicles of Narnia: Reepicheep, the other Talking Mice, and the Dwarfs in the various Narnia films. (see Literature)
Lori Campbell (Monica Keena) in Freddy vs. Jason. 5'1", and she decapitates Freddy Krueger with a fucking machete! But not before setting the dock on fire, blowing Freddy and Jason into the water.
Jason White from Superman Returns. He starts off as a wheezing asthmatic child, child of Lois Lane and her new squeeze. Then crushes a mook with a thrown piano when said mook threatens his mother, proving that his real father is Superman.
Sir Didymus in Labyrinth. He's a fox that rides a mid-sized dog and is an aggressive fighter, as well as a noble knight. The knight part means he's lacking a bit in the common sense department at times.
In Real Steel, Atom is an old robot a few generations behind the current fighters. He is also considerably smaller than them. With some modifications by Max and boxing training by Charlie, Atom is able to own most of the competition.
Chucky of the Child's Play series is of course, a doll, which means he only reaches about knee high. But as several of his victims have found out, his small size doesn't mean he can't mess you up.
Luther, played by 5'6" David Patrick Kelly in The Warriors. While his outward personality is that of an obnoxious pest, he's actually a very dangerous individual, as you can work out from the "Oh, Crap!" expressions on the Warriors faces when he shows up at their hideout.
Hit Girl from Kick-Ass is eleven years old and is able to mow through a small army of trained adult killers by herself, a pint-sized one-girl-army.
Mark Wahlberg in just about anything. He's 5'7" and almost always plays a total badass.
The titular character in Ant-Man. After being shrunked down, he retains his density, meaning that the average strength of his punch focused on an incredibly small surface makes him act like a bullet. In fact, he has to learn how much strength he has to apply in a single punch so as not to kill everyone he attacks.
Negasonic Teenage Warhead in Deadpool is a small teenage girl whose powers basically make her a human bomb.
Tinkerbell in Hook manages to take down several pirates effortlessly.
Parodied in The Three Stooges short Punchy Cowpunchers. When each of the mooks tries to take away the heroine Nell (played by Christine McIntyre, who was about 5'2" in real life), he gets knocked out with a single punch. And in true ladylike fashion, Nell faints after each struggle.
Rocket Raccoon in Guardians of the Galaxy, as long as he has a gun with him (which also tends to be just as big if not bigger than him).