Sakura of Naruto learns it from Tsunade, who also breaks the ground with simple punches - Tsunade in her true form is actually a frail elderly woman with even less muscle size than Sakura. This Super Strength is apparently achieved by perfect chakra control.
Hinata also falls into this category in a way; her clan's specialty is the "Gentle Fist" technique, which rather than using crippling damage delivers a short, intense burst of energy to block a chakra point, preventing the use of ninja techniques (and potentially the use of limbs, or *organs*). In the anime, she's also shown the ability to improve the "near perfect defense" technique to a "truly perfect defense", and turns the Gentle Fist into something that would make Kenshiro start to shed Manly Tears. At least, she does this occasionally. Hinata would probably be stronger were it not for her absolutely crippling self-esteem issues, which are only sporadically overcome by following Naruto's example.
Yachiru Kusajishi of Bleach is able to carry her captain, Kenpachi Zaraki, without much trouble despite her being about 33 pounds (15kg) whereas he weighs in at a Tyson-esque 237 pounds (108kg).
Ururu, the little girl that helps out at Kisuke Urahara's shop, also deserves a mention here. When the arrancar first invade the real world, she snaps and starts kicking ass, much to everyone else's shock. She also showed off some of her skills back during Ichigo's Training from Hell.
Sui Feng is the captian of Squad 2. She's under 5-feet tall, fast as hell, and her zanpaktou is essentially a hornet's stinger. At least until she unleashes her bankai, which turns it into a giant missile that she hates because it's no good as a weapon for an assassin.
Also Yoruichi, who is known as the "Goddess of Flash" and laid Yammy Rialgo out with no help at all. She also gets points for drilling Aizen into the ground not once, but twice.
Can we say Hiyori Sarugaki? Despite, according to her bio, weighing 57lbs and standing a grand total of 4'4" tall, she is not only an Vizard, but was the former 12th division lieutenant and she regularly smacked Ichigo around.
Slender fifteen-year-old Kaoru Konoe of Gate Keepers has the ability to heft battle tanks and throw buses for hundreds of yards, thanks to her Gate powers.
Shinobu in Urusei Yatsura displays low-level super-strength when sufficiently provoked. This developed from what was originally comic relief slapping and hitting.
Asuka of Neon Genesis Evangelion displayed this trope in the manga version. After bumping into a gang member in an arcade, she manages to easily kick him out the way and hold her own against several other big, burly men alone, with backflips and all. Admittedly she used the "Look Over There!" trick first. She never displays these moves again in the series, apart from a brief moment near the end of the same book.
Yuno Gasai of Mirai Nikki. Holy.Freaking.CRAP. She's a fourteen year old girl, and she's capable of slicing full-grown men twice her size clean in half. She racks up the highest body count in the series by a mile, all while wearing her rather terrifying trademark cross between a Moe Stare and a Slasher Smile. She's the very definition of this trope, among others.
In the case of Gally (or Alita, depending on who you ask) from Gunnm/Battle Angel Alita one would argue that her being a Full Conversion Cyborg justifies this... except that the vast majority of her opponents are as well, and are almost invariably much bigger than she is (frequently by a factor of 10 or more) and often just as advanced or nearly so.
Also, as Gally/Alita herself states at one point, Panzer Kunst (her fighting style) was created to fight larger opponents, specially larger cyborgs.
In a flashback scene in the manga, it's explicitly stated she's special, being one of the best practitioners of Panzer Kunst, and made all the more exceptional because she's female.
The Little Miss Badass of Mahou Sensei Negima!, Evangeline A.K. McDowell, fits this well. During the Tournament arc, she tosses around all her opponents with ease using Aiki-jujitsu, a real martial arts technique, and strings. Using the two, she completely pins down Setsuna, who is one of the strongest characters in the main cast. But then she is a 500-year-old vampire, and has been learning the art for the last 100 years or so.
It's even implied that she learned the art from the man who originated it.
In Blade of the Immortal the deadliest swordsman is not Manji, the immortal main character, or Anotsu, the Big Bad, but Makie, a skinny, waif-like former prostitute who killed sixty wolves in one night at the age of ten. The trope is ultimately averted when Manji comments on how Makie's muscles are weaker than his and that her true advantage is her speed combined with her skill that she use to give her segregated Blade on a Stick more power through sheer momentum.
In episode 18 of the Tenchi Muyo!OVAs, Sasami—armed only with a staff she apparently kept in her hair—effortlessly defeated an armed and highly trained Galaxy Police operative, despite appearing to beno more than 12 years old and having shown no martial prowess whatsoever at any prior point in the series.
It's All There in the Manual. Sasami does possess martial arts prowess, it just wasn't mentioned in the OVAs before — after all, her mom is the head of Emperor's security and uncontested martial arts champion of the whole Jurai Empire. And it was mentioned in the supplements that Sasami DID train with Misaki, so she could take out a couple of GalPol mooks even without Tsunami's powers.
Nicely avoided in the anime Noir, adding credibility to a show with a implausible body count in most of its fight scenes. The whisper-thin ur-waif Kirika is one of the two most lethal human beings on Earth. However, the writer never has her indulge in waif-fu. She always uses weapons to make her kills—including, in one case, a plastic high school ID card, never her hands or feet, and rarely shows more strength than might be plausible for her body frame.
Her weapon of choice is a Beretta M 1934, which fires .380 ACP, a fairly small round, typically used for backup guns only. The only common rounds weaker are .32 ACP and .22 Long. Much less recoil than a .45, or even a 9mm, usually.
Of course her sheer ability to dodge bullets, and general use of acrobatics still very much enter her into this category. Ditto for Chloe, who also fights roomfuls of enemies with firearms with only tiny throwing knives.
The titular heroine of the anime Solty Rei is a young, seemingly defenseless, robot girl with a Mysterious Past who "adopts" a bounty hunter who "saved her life" - who is able to take out a fifty-foot mecha piloted by two Mooks in the second episode. With one punch to its fist, which was in the process of trying to punch through her to her adopted protector. You don't want to mess with her.
And don't forget her very next move, where she hurled it into the stratosphere.
Although skilled primarily in the use of firearms, the child assassins from Gunslinger Girl are capable of punching a guy in the face hard enough to break his neck. Justified in that they're cybernetically enhanced to the point of having superhuman strength/speed/reflexes and being virtually bulletproof save for their eyes.
While they are fast and strong, Triela's training scene implies that they are not really that skilled. Triela's the best hand-to-hand, and a burly instructor kicks her butt comprehensively. He then asks for (and gets) two weeks to teach her properly. After which she kills a trained assassin with a two-finger strike.
Averted in The Daughter of Twenty Faces. Although the titular 90-pound heroine Chiko is an Action Girl, her action mostly involves acrobatics and escape, not fighting people directly. Her trainers even point out that she can't hope to fight big burly men directly in hand to hand combat and if she must fight she has to rely on using their momentum against them and the like. Being explicitly told during training to aim directly at the groin area also helps.
Her fighting becomes more Waif Fu-like later in the series though.
Anita of the R.O.D the TV is very strong, capable of stunning a "vampire" by throwing a book into his face breaking his nose from five meters away without using her paper powers, and she can knock out grown men 3 times her size. Her fighting style was developed by animators via "observing monkeys and the Chinese Royal Acrobats." This is likely due to her being created in a lab by the British Library.
Anita was actually the only paper sister in that episode who could use her paper powers because they are simplistic and do not require the paper to take shape and are therefore immune to the subtle sound vibrations that permeated the castle grounds. Didn't she kill that "vampire" by the way?
Anita does this trope again and is also shown to be a walking "Got Milk?" advertisement when she plays sports at school and throws a scorching fast ball across two fields into the catchers mitt.
I believe, in the dub at least, this was further emphasized by the catcher himself, as he said, "Dear God," in a very stunned voice.
Meow from Kazemakase Tsukikage Ran is a very slender young lady, who takes out entire gangs of armed mooks barehanded if sufficiently provoked. She still often plays the role of Damsel in Distress to the protagonist though, if the plot so desires.
Gender inverted in the manga and film Tekkon Kinkreet. The two boys, White and Black, are only skinny, unassuming ten-year-old boys, but they manage to take down grown, gun-wielding adults with nothing more than a length of pipe and some incredible jumping skills.
Technically, all female fighters in Ranma ˝ save Cologne, as they're small, slender Japanese teenagers - and Akane and Ranma themselves are the tiniest of the bunch. Made explicitly obvious when they take on the humongous Dojo Destroyer and Pantyhose Taro.
In the first episode of Pokémon, Misty pulls Ash out of the water with a fishing rod, throwing him over her head in the process. A massive case of Fridge Logic.
In a way, it's subverted later when in an actual contest of strength, Ryuji easily pins her to a wall.
Ayumi from Hatsukoi Limited has the build of an ordinary schoolgirl and the kicking power of a martial artist. Even the thug-like Misao is impressed with her kick.
Eri Kisaki of Detective Conan, in her first appearance, literally throws a muscular opponent three times her size across rooms and through walls. Her daughter Ran is also skilled in karate, but she's more of a Cute Bruiser variety.
A 15-year-old schoolgirl named Saya Otonashi may not be particularly intimidating, but there's a very good reason she's often mistakenly referred to as Blood The Last Vampire.
Intentionally averted in Ouran Highschool Host Club. Haruhi, dressed as a boy, tries stopping two guys messing with some girls. Of course, she's quite short and rather thin, so five seconds later they chuck her into the ocean, and she can't swim either. The host club and Tamaki especially get really pissed at her for it. Some cry Values Dissonance or worse while others call it realistic and a good message.
Values Dissonance can be avoided however by the fact that at the end of the episode, neither Tamaki (who reprimands Haruhi for doing something foolish and dangerous) nor Haruhi (who doesn't see how helping people in trouble could be bad) concede fully to other's views.
One could argue that in that situation the options were three girls in equal amount of trouble, or just Haruhi herself; she did help the others even though that put her in danger instead - and arguably her full intention.
Hunny is a good male example; looking like an elementary student, he's a fierce fighter who once took down six or seven armed and armored private police officers with no weapons, and they didn't even stand a chance.
Magical Girl Lyrical Nanoha Vivid has Vivio, Einhalt, Rio, and Corona, who are all 10 to 11 year old little girls that practice Strike Arts, the Mid-Childan Martial Art. For fun, they play "Who can displace the most water from a lake with a single punch above the water". Einhalt was able to make a five-meter tall waterspout with hers, temporarily making it rain in the area, complete with accompanying rainbow.
In fact, before the series, Einhart spent her days picking fights with experienced fighters who are all bigger than her even when she's in her Adult Form, and all of whom proved no match.
Izumi Curtis of Fullmetal Alchemist. Looks like a typical housewife. But manage to to set off her Hair-Trigger Temper (which isn't real hard) and you're in for a pretty solid ass beating. And you better pray your don't make her angry enough to use her alchemy...
And then there's May Chang, a young teenager approximately the size of a toddler. She kicked the ass of Edward Elric, an uncannily ripped (at least for his size) master of martial-arts and alchemy, as well as that of Ed's brother Al, who is a SUIT OF ARMOR.
In the second half of the first episode of Kimagure Orange Road Madoka shows how well deserved her scary reputation when she takes down about five times her mass in juvenile delinquents intent on beating up Hitomi-chan.
Itsuki of Heartcatch Precure is a judo practitioner (her grandfather owns the school and she was planning to take over when her brother fell ill). She effortlessly tosses Kumojacky over her shoulder during an encounter way before she became Cure Sunshine!
Koneko of High School D×D is the shortest member of the group, and looks like she should still be in grade school. She also has the power of The Rook, which supernaturally enhances her strength several times over and makes her the team's muscle. In practice though she tends to wind up on the receiving end of The Worf Effect.
Attack on Titan features a large amount of this, as people who fight the Titans (which range in height from four to fifteen meters) have to make use of Le Parkour if they want to strike their weak points without getting eaten.
Annie Leonhart likes to claim that she's just a "weak maiden". Eren points out her tendency to curb stomp guys literally twice her size as evidence that this is a blatant lie.
Mikasa, who is still slender, is also shown to be very muscular under her clothes. Her washboard abs are something of a meme amongst the fandom.
In a late chapter of Bone, Thorn effortlessly lifts a Vedu warrior (easily twice her weight) over her head and throws him, presumably aided by her powers as the Awakened One. Then a squadron of 15 Vedu warriors appears and beats the tar out of her.
Hit-Girl in Kick-Ass. She is trained in martial arts and firearms as well.
Given the vagaries of comic book art, just about any unpowered female will probably use this at one time or another, as quite a few artists simply refuse to draw women who look like they could carry a milk carton, much less win a fight. Combined with a tendency toward hyperthyroidism in male portrayal, this led to some especially egregious examples of Waif Fu in the 90s.
Lois Lane has a Military Brat background, which helps explain why she can get away from the occasional mugger on her own, but it was carried to ridiculous levels in one story when she single-handedly storms a guerilla base commando style to save a Brought Down to Normal Clark.
Sin City has Miho, who is described as being 90lbs and barely clearing 5 feet. She has thrown men through the air with her kicks and is strong enough to leap off a rooftop and shove swords through a car roof.
Apparently, she's one of the "gods" of Sin City. Being a deity might be the only way to explain her 90 foot vertical or surviving a grenade going off under her feet without a scratch.
Spider-Man himself provides a very rare male version of this. Due to his powers, he often dances around his opponents without getting hit. This is more obvious when fighting the likes of the Hulk or the Rhino.
Song in the Image comic book Epic Kill is shaping up to be this. As an individual who doesn't really use weapons, she's considered a national security threat.
An unusual take on this is The Wasp and Ant-Man, two characters whose primary ability is to shrink down in size. Henry Pym devised a form of martial arts that takes full advantage of being several millimeters tall while retaining normal human sized strength and mass. Wasp plays it slightly straighter, being that, even at normal size, she's just over five feet tall and learnt how to kick ass from Captain America too.
Firefly: In the comic Better Days, River kicks an Alliance commando in the teeth while he's sneaking up on her. Without looking.
Dash in The Incredibles beats up the security guards on Syndrome's island, and it's clear that he isn't 100 pounds even when soaking wet. At one point, a guard lands a direct hit and sends him flying.
Films — Live-Action
In the movie Kick-Ass, the heroine Hit Girl takes this to Matrix like levels of combat skill. She is by far the best fighter in the film, much more skilled than the protagonist.
The quote above comes from the Firefly movie Serenity, where River's Super Soldier programming forcibly implanted by The Government manifests when she receives her activation signal (a "Fruity Oaty Bars" commercial) at the Maidenhead bar. She proceeds to wipe the floor with everyone in the bar, including resident Big Guy and Badass Jayne, who takes a shot at restraining her but gets a painful Groin Attack and a serving tray to the head that knocks him flat for his trouble. She is only deactivated when her brother Simon speaks a code-phrase that serves to knock her out. Her impressive capabilities come from a combination of Psychic Powers, extreme intelligence, and intense conditioning, which drove her insane. That's not even mentioning what she does to the Reavers at the end of the movie.
Dragons Fire And Ice: Kyra, who looks like a series of toothpicks in a red catsuit and only 5 pieces of armor plating, fights against a massive horde of exceptionally large Vorgans.
Also, the whole Eighth Drunken God's being the most bad-ass and being a woman flaunting her body, with moves such as "putting on make-up" and "pretty girl looks in mirror". Although in some versions of the actual myth, "she" is actually a man in drag.
Subverted hard in The Losers. One of the Losers fights off a woman, and she's just as hard as nails as he is, and both fight really dirty.
Pretty much every martial arts film starring 5'3" Cynthia Rothrock. Rothrock is a multiple World Karate champion (although technically in forms and weapons demonstrations, not matches), and in most films will get the stuffing beat out of her by much larger bosses or Dragons before eventually emerging victorious. Rothrock herself has said that her movies are just movies and that a similarly skilled man would beat her every time in real life.
One of Sandra Bullock's early roles, in Demolition Man. She takes out one of the big strong super-violent thugs with a single kick. And how did she learn this move, living in the ultra-pacifistic society that has outlawed violence? She watched a Jackie Chan movie.
3 Ninjas. Despite the fact that the main characters were kids and not girls, they used the style. And one of the sequels had a girl who excelled at Waif-Fu to the point that she curbstomped one of the ninjas in a tournament fight.
Chocolate (2008). Zen, a small Thai autistic girl whose Disability Superpower is to absorb martial arts from movies and TV shows. The entire movie is her beating up hundreds of people larger than her with muay Thai. The actress supposedly spent 2 years learning enough muay Thai to make it look realistic. The film handled her smaller size well - often, she uses it to her advantage by taking the fight into narrow spaces where her opponents have trouble moving.
Kate Beckinsdale's Selene in the Underworld series. Her counterpart in the prequel, Rhona Mitra's Sonja, however, is a Faux Action Girl.
The teen/tween in the archive in Blade. She looks about 12 or 14 and she kicks Blade so hard he falls back. She even plays helpless, scared and cute when he first sees her, then kicks him through some Soft Glass.
Presumably due to Unstoppable Rage, the titular character in Blood Night: The Legend of Mary Hatchet manages to kill at least six asylum employees (five of them orderlies and/or security guards) barehanded. It's averted in the case of her daughter (played by the tiny Danielle Harris) though; once disarmed, the Final Boy easily overpowers and strangles her to death as she rather ineffectively wails on him.
In Iron Man 2, Natasha Romanova blows through a building with a combination of non-lethal weaponry and improbable martial arts - all in the time it takes Happy Hogan to take down one guard with conventional boxing technique.
Happy is at least enough of a bad ass boxer to be Tony Stark's bodyguard in the comics (until Iron Man got the job) while in the movie he is relegated to "put-upon chauffeur." Naturally, he's not match for Waif-Fu Lucha libre moves.
Also, in Iron Man 3, Pepper Potts is suddenly able to do this, courtesy of experimental drugs that enhanced her strength.
Loki in Thor is a borderline male example- he's played by 6' 2", ordinarily-slender Tom Hiddleston, but made up and costumed to look outright skinny- and still capable of at least briefly beating his beefy brother's ass in combat (including, notably, using his father's scepter/spear as a pole to propel his body around in order to increase his momentum for a kick in the face).
Selina Kyle in The Dark Knight Rises, though the disarming front she presents is more psychological than physical- she's played by 5'9" Anne Hathaway. It's not so much that she's tiny as it is her ability to come off as meek.
Alice (Milla Jovovich) in the Resident Evil movies takes this to ridiculous extremes, with even an unpowered Alice sending full-grown adults (and zombies) flying with moves straight out of The Matrix.
Penryn, the heroine of Angelfall, a starving teenage girl, fights trained soldier Boden with her various martial arts techniques.
Lisbeth Salander in The Millennium Trilogy is 4 feet 11 inches tall and looks like a child. She's no ninja, but happens to be very good at avoiding getting hit, sneaking up on people, and incapacitating her opponents, whether it's with stones, golf clubs or nail guns.
Lieutenant Karrin Murphy in The Dresden Files is 5 feet tall and a hundred pounds soaking wet. She's also The Big Guy. This is because she's highly skilled in aikido, which uses an enemy's weight and momentum against them.
And it goes Up to Eleven when she picks up one of the Swords of the Cross, especially in Changes.
Although, on some level, also averts it. In the short story "Aftermath," which is told from her perspective, mentions that she's mastered several different martial arts (Aikido, Wing Chun, Jujitsu, Kali, Savate, Krav Maga, Tae Kwan Do, Judo, Boxing, and Shaolin Kung Fu,) she also mentions how size and strength go a long way. She's mentioned that, despite her skills, she (like most women) always walks around with a slight nervousness in knowing that half of the population could easily overpower her.
There's also "Lydia", the mysterious client in Grave Peril - when possessed by a demon, she's easily able to throw Harry around, even though he's much bigger. Being Harry, he comments that this shouldn't work.
Mariel of Redwall. She's a mouse, probably aged about twelve in the first book, and has been kept as a slave for quite a long time, yet she's able to beat up seabirds with nothing but a length of knotted rope.
A lot of the Dibbuns, most prominently Baby Dumble, who was fighting crows in diapers. (Though admittedly he wasn't actually very good at it.) Or Bragoon and Saro, who left home to kick ass when they were still Dibbuns and don't come back 'til they're old, after which they kick more ass before dying epically.
Justified in R.A. Salvatore's The Cleric Quintet with Danica Maupauissant. She's described as "barely topping 5-ft and 100 lbs., with a mop of bouncing strawberry-blonde hair." And she kicks the tails of everyone. Priests of Oghma, who are very accomplished wrestlers (and most are at least three times her size) make her wrestle them before they tell her where to find what she wants in the Edificant Library. She always wins. The reason this is justified within the series is because she's a Dungeons & Dragons 2nd edition Monk. Loosely translated: Shaolin monk on crack.
Nellie of The Avenger. Weighs maybe a hundred pounds sopping wet, tosses men more than twice that weight easily, thanks to her extensive knowledge of jujistu and other martial arts. Her job is made easier by the attitudes of the 1930s making it hard for male opponents to realize how effective a combatant she could be.
Vin has an advantage even over other mistborn, not just because her small form gives her greater agility and balance, but because her super-strength is more concentrated, giving her a proportionally stronger punch. She basically uses the Square/Cube Law to her advantage. Her small size is also useful for stealth, since mistborn are typically assassins and spies. The only disadvantage is in the manipulation of metals, since if one is too heavy she will be moved instead.
Though it should be noted that she is still weaker than a muscle-bound bruiser with the same powers as her, which bites her in the behind at least once when she gets pinned by such an opponent.
Bast the Wood Elf John Ringo's Council Wars series who's about five feet tall and looks like a fourteen-year old girl although she's not. Justified in that she's a genetically engineered killing machine with about a thousand years of combat experience.
The Vord Queens in the Codex Alera series look like slender, beautiful women due to the fact that the original was exposed to Kitai's blood and thus was altered in the first book. They are also incredibly fast and strong and are able to take hits from titanic crossbows that can punch through heavy armor or horses and keep going. Then again, they're not human, but the powerful, monstrous leaders of a species that has eaten entire worlds.
Also, Kitai, a young girl with the strength of a grown man and the ability to take almost anyone in a fistfight. This is justified by the fact that she's a Marat, not a human, and she's pretty well-muscled to boot.
Matty Roh of The Heritage of Shannara is quite tall, but her slender build and reliance on a rapier make her fit this trope. Her strategy relies on dancing around her opponents before going in for the kill. Makes things rather interesting when she teams up with the much more physically powerful Morgan Leah.
Jacky Faber of Bloody Jack fame often uses her skinny young waif act to get out of tight situations. Most of her adversaries who fall for this are fooled into thinking she's a Just A Girl, to their detriment, since she's a former street rat/war veteran with a "shiv."
Dairine Callahan from the series. At eleven she offers to take on her fourteen-year-old sister Nita's biggest adversary, Joanne, and beat her up (Joanne and her cronies had just beaten Nita up pretty badly)— and although she doesn't do it, it's made quite clear that she can, and even Nita admits it.
Nita and Kit are both also examples. The reason Nita doesn't fight back is that although she has the skills, she knows that she's outnumbered and fighting back will only make it worse. But when she gets a hold on wizardry she gains self confidence— and a much, much bigger adversary than Joanne. And she kicks butt. And the magic is just as cool as physical skill, because fighting with magic costs you just as much energy and strength as fighting physically. Magic is just more... dignified. Well, aWoM kind of subverts that in Nita's battle with Aurilelde, but still.
YW has so many examples of this, you can't name them all.
The Valkyrie of Immortals After Dark live and breathe this trope; as one of the books puts it, they are "small and delicate-looking. It's a biological advantage. You'll never believe what they can bring to a fight".
Nico from The Spirit Thief in the Legend of Eli Monpress series. She's small and painfully thin, but her demonseed abilities give her inhuman strength, speed, healing, and the power to step through shadows.
Tris from the Divergent series. It's continually pointed out how nobody thinks of her as a threat (especially at the beginning) because of her tiny frame and stature.
Played realistically in the Belisarius Series: Shakuntala is extremely fast and nimble, the prize pupil of India's most lethal martial artist and phenomenally strong for her size. However, she is tiny (about 90 pounds soaking wet) and that bites her on the arse a number of times.
Ninette from Reserved For The Cat; she's a trained ballerina, and knows that jumps, spins, and kicks can be useful both in dancing and fighting.
Tuon from The Wheel of Time is a petite bald woman who can be easily mistaken for a little boy, but it would be ... unwise to underestimate her ability to kill you with her bare hands.
Arya from A Song of Ice and Fire novels is a bit of a subversion. In the first book, she is specifically trained to fight in this kind of style, but attempts to take on actual experienced and armed male combatants throughout the series usually end with her being disarmed readily. Fortunately, she is able to actually kill many of her targets using skill and trickery, mainly by exploiting the fact that no one tends to think she's capable of killing them.
Ami from Dianne Duvall's Immortal Guardians series is five foot one...and yet she took down dozens of vampires in one fight. Of course it helps that she's been trained by people who literally have centuries of experience in fighting. And her enhanced healing abilities and other perks of being an alien from the planet Lasara don't hurt either.
Oana Constantinescu from Mr Blank, the bronze medalist in the women's gymnastics all-around in Sydney, is a practitioner. She's not really described as slender — she's a solid block of muscle — but it's repeatedly stated that she's roughly hobbit-sized.
Ingrid Brady in Get Blank is a kung fu master, though it appears to be because of her physique rather than in spite of it. Her skinniness is because of a bizarre ascetic commitment and appears to have given her slightly superhuman strength, agility, and reflexes.
In the Gentleman Bastard series, Gender Is No Object, so female fighters are just about as common as men. Many of the female toughs encountered are described as being skinny or downright petite, yet this never seems to be a detriment to their fighting abilities.
Happened to Lana Lang in season 8, with the very brief and none-too convincing explanation that she had taken a self-defence course. She had had a waif-fu moment as early Season 4, but she was possessed by Isobel Thoreaux, a Wicked Witch and Dark Action Girl, at the time, thus justifying it at that time.
Lois is also prone to this, although it's somewhat more believable thanks to her Military Brat status, although it is still stretching things a bit as she basically beats anyone without a gun, and would knock the gun out of the hands of whoever has one.
In Season 10, Chloe Sullivan unfortunately becomes the least convincing one after returning from being off the grid, not even having anything to handwave her sudden fighting skills that allows her to defeat multiple secret agents with guns without breaking a sweat.
In the Doctor Who episode The Mind Robber, Zoe gets the super-powered Karkus to work for her by defeating him in hand-to-hand combat, despite being much shorter, having no powers, and showing little tendency towards physical combat before. One explanation is that they're in a dimension where Your Mind Makes It Real, and Zoe doeshave a very good mind.
Alternatively, she had seen the Karkus is comic book form and knew he didn't truly exist, so he had no power over her. The Doctor had never heard of him, so he wasn't able to fight the Karkus the same way, but he could confidently claim that the Karkus' "anti-molecular ray disintegrator" gun was complete rubbish and couldn't possibly work, at which point it ceased to exist.
The titular character in the episode The Doctor's Daughter displays this.
Anji from the Eighth Doctor Adventures has met thirteen-year-old girls who are taller than her, but in Timeless she basically functions as a bodyguard to a man whose friends, family, and acquaintances have started attacking him. And none of them stand a chance against Anji Kapoor, petite futures trader and surprise badass.
Cameron in Terminator: The Sarah Connor Chronicles. Justified by the fact that she is a Terminator. Cameron is played by Summer Glau, the same actress who played the "90-pound girl" seen in Firefly. Interestingly enough, Cameron's small size when compared with other Terminators does actually play into the fight scenes; when she tackles another, larger robot in a straightforward slugging match she typically loses unless someone is helping her. It's only when she outmaneuvers or surprises a Terminator (for example, the "water delivery" Terminator, or Stark, or Cromartie the first time) that she wins without outside assistance.
Fiona from Burn Notice is a small girl and no stranger to combat, but this trope is averted as she is a Combat Pragmatist. On one occasion she was supposed to take down a large man to interrogate him later. She tried using a stun gun but he disarmed her in the attempt. She managed to get it back while he was trying to wrestle her down. After the narration explained that stun guns will shock you if your target is holding onto you, Fiona proceeded to stun the guy anyway.
Echo, Sierra, and November from Dollhouse depending on what imprint they're loaded with. Although even in fights where Echo has the right imprint, she still gets her small size used against her, as in she gets picked up, carried and shoved or thrown against something. In one fight to the death Sierra got into it was half luck that she escaped alive. November seems not to feel pain in assassin mode.
Sam of iCarly despite being a 5-foot tall tweenager, is somehow strong enough to take down several security guards, a girl bully much taller than her, and move a giant piece of a destroyed wall with one hand.
Robin on How I Met Your Mother appears to have this ability, throwing down Ted in one episode. Then again, Ted has been shown to be an extreme example of Non-Action Guy at times, so it's not that great an accomplishment.
Parker in Leverage: Normally avoids combat, but cracks open a case of waif fu to fight a Serbian gangster. As per the trope, when he gets a grip on her she's in serious trouble, but when she breaks free she's able to use her greater speed and agility to knock the crap out of him. Although later in the series, she seems to primarily use stun guns whenever she needs to engage in combat. Though she is able to deliver a beatdown to protect Hardison.
Pick any of the female Power Rangers. They tend to be◊ noticeably◊ shorter◊ than the male rangers, but they can hold their own in a fight, even with the occasional kidnapping.
My Name Is Earl: Joy Turner may come off as a typical trailer park mom, but years of Springer and a mean right hook make her a force when she gets really pissed. Just ask Earl's ex, a trained bounty hunter.
Samantha Carter of Stargate SG-1, while 5'9" and so not precisely short, is blonde, adorable, shorter than all her SG-1 teammates by at least three inches, and at least twenty pounds lighter to boot. And yet she kicks at least as much ass as they do on a regular basis. Remember when she blew up a sun??
Phoebe from Charmed does this occasionally but it's justified since she'd been shown practicing martial arts. In a few season 3 episodes Prue gained this for no apparent reason, even with Piper trying to keep up. Unfortunately these scenes are made rather unconvincingly.
Sydney Bristow in Alias. Even though Jennifer Garner isn't exactly a runt.
In "Game of Death", an animated short featuring the band Gorillaz, Noodle (a 10-year-old girl) effortlessly throws Russel, who is extremely large.
Prior to Gail Kim's original WWF debut, there were plans to bring her to compete against the guys using her waif-fu like high flying abilities. Unfortunately, there's a difference between hype music videos and actually performing in the ring, and while her moves may have been impressive, her unreliability at hitting them properly and consistently (read: she botched a lot) put an end to those plans.
WWE also had plans to bring Shantelle Taylor in wearing a bodysuit, win matches against guys, and reveal herself as a girl after she'd been winning. They never did this, however, and she ended up wrestling in TNA as Taylor Wilde - then retiring because of how little money she was making there.
Ivelisse Velez used this whenever she competed as a face in intergender matches on the independents.
Rey Mysterio whenever he's up against larger opponents. Though he's actually larger than most normal men, he just looks like a dwarf next to the much huger big guys. Ditto for Evan Bourne.
Current WWE Divas that employ this style - Kelly Kelly, Alicia Fox, Eve Torres, AJ Lee and Naomi. In Eve and Kelly's case it's justified since they're both former gymnasts (and Eve is a blue belt in Brazilian Jiu-Jitsu) while Naomi is a former dancer.
That said, these games will provide systemic support for this, with smaller characters having bonuses to dodge and hit larger characters whose advantages lie in their superior reach and damage.
The earliest edition of D&D made some effort to avert this trope, as maximum weight allowance was also dependent upon character weight. Furthermore, the Strength scores of characters were limited by race and gender. For example, human females were limited to 18/50 Strength whereas their male counterparts capped at 18/00. For the other races it was a bit lower. Female elves were limited to 16 Strength scores, and female halflings could have a maximum allowable Strength of 14. However, there was no imposed penalty in rolling for their initial abilities.
Warhammer 40,000's Eldar, despite being thinner than the average human, are at least as strong as one. This is explained partly by different muscle configuration, and partly by their speed; since net force equals mass times acceleration, this means that they can actually hit fairly hard, even if their lifting capacity is not all that great.
Played with when considering Aspect Warriors like Striking Scorpions, who wield chainswords that increase the strength of the wielder, Farseers and other special characters.
Effectively canon in BattleTech and more specifically the RPG version Mechwarrior, where player characters can take significant risks to bring down Battlemechs on their own. The canonical example is Cassie Suthorn of the Camacho's Caballeros mercenary regiment, a petite woman described as unable to weigh a hundred pounds without wearing a soaking wet bathrobe first. She knows the agile and evasive Indonesian martial art pentjak silat, and the skills that come with knowing the art have proven handy in helping her hunt and kill enemy 'Mechs more or less singlehandedly. She has a kill count of over a battalion of Battlemechs of varying weights without riding one of her own—it's noted that the vast majority of her 'Mech-piloting comrades, even the ones in Assault 'Mechs, don't have a kill record that high. She is also no slouch in hand to hand combat, regularly defeating the setting's equivalent of Secret Police Space Ninja.
Sakura Kasugano from Street Fighter and her rival, Karin Kanzuki, who is out to prove that her Waif Fu is stronger than Sakura's. Canonically, she succeeds, but decides that the real importance lies in the thrill of the fight.
In the Soul Calibur series, petite pre-teen Amy can apparently block blows from weapons delivered by enormous men wielding axes, swords and maces.
Used to hilarious excess in The Misadventures of Tron Bonne. After declaring how she'd been taking self-defense courses since the last time they met, policewoman Denise proceeds to manhandle Tron's Humongous Mecha by judo throwing it around town.
Also Colette from the same game. You don't see as much of it with her as you do with Presea, but if you can watch her pick up a huge, muscular man that probably weighs twice as much as her without ANY effort whatsoever, then say she isn't strong, you're insane. Granted, she has angel powers, but still, it's damn impressive.
Tohsaka in Fate/stay night. Look at her twig arms and mediocre height and tell me, do you honestly believe she could pull off the admittedly awesome things she does in hand to hand combat? Also Saber, but to her credit when she isn't buffing herself with magic strength she's actually a good deal weaker than either Shirou or Tohsaka. It'd be even harder to believe otherwise from her considering she's about five feet tall and weighs ninety pounds.
Of course, in Saber's case physically weaker doesn not reduce her insane skill.
Both of them use magic power to compensate for lack of strength. And in Tohsaka's case, to get around an opponent (Caster) who's otherwise immune to pure physical attacks.
Ciel from Tsukihime usually just chucks swords. Okay, kinda believable. But then she lugs around a gun that weighs more than she does, and it doesn't seem to slow her down that badly? Uh, okay. At least Arcueid is a vampire and has magical super strength or something. Actually, Arcueid admits outright that most of her strength has nothing to do with muscle mass and only considers herself as 'athletic' without it, enough to dodge Shiki's knife if he were to try something.
Konoko, the slightly-built protagonist from Oni, makes a habit of beating up on burly stormtrooper types.
Just about any fighting game allows even the smallest girl to throw the biggest and fattest man. One example would be the Dead or Alive series where you can kick/punch/throw a character into a wall (or right through it, breaking the wall) from quite some distance, or down to a lower stage, defying the laws of physics. Here's a demonstration.
Penelo from Final Fantasy XII is very petite compared to the rest of the party, but she can be formidable in her own right, and you can even give her a BFS.
That said, her stats do favour magick rather than combat, so it's up to the player's discretion. Fran is perhaps a straighter example: she is basically a playboy bunny species, and (in cutscenes and quickenings only, natch) shows dexterity and martially artistic moves.
In Tekken female characters tend to be equally sized, but Xiaoyu is probably the smallest, yet is a very tough - and quick opponent.
There are also have Gnome and Goblin females in World of Warcraft who are just the tiniest of the females out there in the Alliance and Horde respectively. But when played as a warrior they become tiny titans who can tank raids as well as any Draenei or Tauren male... the largest player characters possible on the same sides of the fence as the aforementioned females. And with the application of the proper talents, these mighty minis will wear full plate armor, and wield a gigantic two handed weapon in each hand, all the while moving like a ballerina on the battlefield. Not to mention what they can do with straight up DPS as rogues, death knights, or other melee combat classes. Forsaken females may also qualify for this trope as well when one considers that there is literally little left to them but skin and bone, looking as if they could fall apart with a good hit from a thick stick. Granted, the difference in size can be completely negligible compared to some bosses such as dragons, demons, elemental lords and the occasional Humongous Mecha. Each of these looks like they could crush an entire raid group with one stomp, thus making this trope apply to just about everyone.
Skyrim. Bretons and in the previous game, Wood Elves, are both smaller then many of the other races, but can prove just as competant in melee combat if built right.
Female Elves and Dwarves in Dragon Age are both much smaller than Humans (either in build or height), but aren't to be reckoned with. The Warden in particular. Subverted in Dragon Age II - Merrill (who is very small/thin) is a mage, but she can be built to withstand a lot of punishment (making her a weirdly effective Stone Wall), especially compared to Anders, the fragile human male mage.
No one is saying The Boss from the Metal Gear Solid series is a waif, but compared to Volgin, she is lighter, a little shorter, and has 10 millions less volts of electricity flowing through her. None of that stops her from throwing him to ground very easily. In fact, the only time Volgin is visibly scared is when he inadvertently insults The Boss. Also of mention is Paz in Peace Walker, if Snake is too...forward on their date, she sends him flying with a slap.
City of Heroes allows you to make any class any size, but since they can all kick ass it's not impossible to meet up with tiny female front-row fighters.
Most videogames with a only one female boss usually has them as extremely skimpy and waify...and then came YelenaFedorova of Deus Ex: Human Revolution. The only thing vaguely resembling Waif-Fu is her counter for a melee Takedown...which is a kick to the head by a cybernetic leg.
It also helps that you can actually see that she's physically toned and has cybernetic legs that raise her height by a good foot or two.
Twice Blessed has Pella Brightwing, a pixie warrior princess who in her first fight in the comic takes out two robots the size of houses.
Miho. In addition to various improbable acrobatic feats such as dodging an electric ray, disabling it, instantly vacating the scene in a matter of seconds, and walking quite calmly on telephone lines, she also grabbed a car by the hood and crushed it by flipping it over with one hand.
Yuki as well. Although she has not displayed excessive strength or combat skills she also can walk normally on telephone wires (until she realized where she was and promptly fell). She also apparently possesses the power of teleportation which she used to steal, among other things, a whole rent-a-zilla...twice. She also defeated a small horde of Zombie Rangers by throwing appliances at them. Including a washing machine. A remarkable feat, considering most conventional weapons would most likely have been unequal to the task. It has been directly stated that Yuki is indeed a Magical Girl, as always suspected. Very likely Miho is one as well.
Rain from the webcomic Triquetra Cats. Even before getting her magic powers she is still a black belt champion in 9 different martial arts (including one not normally taught to humans) despite being a 14 year old girl with the build of a 10 year old girl.
Tristan from Angel Moxie. This is unexplained at first; later she discovers she's the reincarnation of the Warrior, one of the Power Trio destined to save the world.
One of the main female characters of the Polish Kokoart, Kitty, shows her powers at Waif-Fu many times. The first time it's in the 13th and 14th strip ( and ) where after being insulted by calling her "nuts" by the main character, Cherry, she chases him and his friend. Cherry ends up in hospital (2 arm fractures) after being hit with a truck. When the friend (still unnamed after 3 seasons of the comic!) tells her that the truck was maybe just little too much, she responds, "The truck was by accident".
In 'Schlock Mercenary characters are trained in martial arts aboard a 31st century starship. This becomes much more sensible (eight years later, go figure) when an angry mob sets upon a girl engineer whom readers even mistook for a child when she was introduced. She holds a green belt in shotokan karate[[note:*:(green belts are a lower mid rank, someone who knows enough to get themselves in trouble.]] and her clothing is a standard issue set of powered armor. There were pieces on the ceiling...
Lourdes of Mystic Revolution manages to throw novice player L33t Ninj4 hard into a wall, with a whip, from across a gorge. She also hits a Dryad Berserker (claimed the strongest class-race combo in the game world) clear off the ring, with her bare fist. Granted that she is built like a moderator.
In Gunnerkrigg Court, Jones is a small, slender woman who can casually go toe-to-toe with the massive Sir James Eglamore and easily defeat him in close-quarters combat. Of course, the fact that she's an indestructible entity who has been around since the geological formation of Earth helps quite a bit.
A Grey World - Short, skinny, you could mistake her for a 12 year old boy, but don't get on the wrong side of Alexis. Implied LEGO Genetics gives her above average strength. Being absolutely ruthless doesn't do any harm
Ninjai The Little Ninja: Ninjai. Despite being a young kid, he is capable of killing much bigger enemies and surviving things normal people wouldn't be able to.
Toni Chandler (Chaka) is fourteen, female and slender, but her superpower is control of Ki, and the ability to pull extra Ki out of the Earth. In the short story "Duel Damsel", she challenges a superstrong upperclassman who looks like a blond Sasquatch, because of what the guy did to her friend. She pummels him without even using her most powerful techniques. She's also beaten an unstoppable super-werewolf, clobbered people wearing power armor, taken out a superpowered ninja...
If you must mention Chaka, you must mention Chou Lee. Bladedancer isn't even a mutant, just a "baseline" imbued with the Tao, trained in awesome Wudan martial arts skills, and a wielding a sentient sword that can cut anything. She's taken down the same aforementioned ninja, people in armor, demons, cyborgs, random attackers, and just about everything she's fought since she arrived at Whateley. The reincarnated Olympian gods and goddesses decide to take Bladedancer on together. She wipes the floor with them.
Ayla Goodkind (Phase) is 5ft tall and weighs anything from nothing to a little more than a ton, according to her mood. This mutant ability allows her to toss around opponents many times her size. In "Boston Brawl II" she beat up a forty foot giant and then used his body like a flail, much to the other supervillains' regret.
Gwen from Ben 10 is a ten-year-old girl, yet still capable of holding off the Monster of the Week on her own if needed, thanks to some martial arts lessons.
Starfire who was much stronger than the much bigger, cybernetically-enhanced Cyborg. Interestingly, this was explained as not being a superpower inasmuch as an ability of her species.
Robin is closer to fulfilling this trope, as he is explicitly a slim, adolescent Badass Normal who can toss around a super-strong giant made of concrete as if it were styrofoam. Though, that giant wasn't actually trying to beat him.
The heroes of the Sonic Sat AM cartoon were realistically limited for the most part; but Sally Acorn periodically managed to jump-kick or toss a seven-foot robot in a way that a three-foot rodent probably shouldn't.
Jade Chan of Jackie Chan Adventures through some yet-to-be-discovered law of physics is able to bring down people fairly easily at times. One time she brought down a strong government agent in one kick that her uncle was having trouble with. She brought the big sumo Tohru down in one kick as well, causing the house to shake. Despite all this she still has to be contained by the villains and/or Jackie. This is probably due to her being the reincarnation of the Dalai Lama. Zig-zagged, since there are also running gags where she'll attempt this only to be caught and held harmlessly in the air where she can't get any leverage.
Kim Possible calls on "sixteen kinds of kung fu" and a lot of cheerleading practice to batter armies of henchmen twice her size — despite her looks, she truly is that strong.
Toph is a little, BLIND 12-year old. She routinely kicks everyone's tails. In fact, the only fight she's ever in where she loses is against the protagonist, and that's only because she had never fought an Airbender before. Hell, the only time she ever really gets injured is by Zuko, when she walks up on his camp, and is caught by surprise by his fiery defense. It's true that she almost never makes direct contact with those she fights, and uses Earthbending instead, but still. Hell, she's the most powerful and talented Earthbender in the entire Avatar universe. In the final episode she metal bends the bridge door of a Fire Nation's zeppelin, wraps it around herself as a second layer of skin, and becomes Iron Kid
Ty Lee has no Bending ability, she carries no weapons, she's a skinny perky cutie ... and she can totally incapacitate you by hitting you in the pressure points while remaining impossible to hit.
Then there’s June. She’s a badass bounty-hunter, who can effortlessly beat a man twice her size in arm-wrestling.
To a lesser degree, the Kyoshi Warriors when they aren't under the Worf Effect.
Valerie from Danny Phantom is a minor version being a girl but reasonably hefty. Aside from being stated to be a ninth degree level black belt (despite being only fourteen), she routinely kicks powerful ghosts' butts on a daily basis. At one point she engaged combat on her own battle suit, possessed by a ghost (and managed to hold herself in said battle pretty durn well).
Sue Ellen from Arthur is only 8 and one of the smallest kids in 3rd grade, yet has good enough martial arts skills that she can flip Binky, the biggest and heaviest kid in her class, as if he weighed nothing.
5-year-old Mackenzie from Rocket Power once threw Twister into the air and punched out Lars.
Ahsoka Tano from Star Wars: The Clone Wars first did this to Cad Bane, after he knocked her lightsaber out of her hands, and later when captured and disarmed by Trandoshan hunters, she defeated three of them this way (not all at once). Said Trandoshans are capable of fighting Wookies hand-to-hand if needed.
Rarity on My Little Pony: Friendship Is Magic is a delicate fashion designer and obsessed with high society. That doesn't stop her from beating down Applejack (Physically the strongest of the Mane 6), or knocking out a changeling with one well-placed sucker punch.
It's worth noting that a skinny but skilled female martial artist will more often than not wipe the floor with a huge but unskilled man. Experience does count towards the end result. Of course, a real fight favors real experience, with say a long time bouncer often being better prepared than a no-contact karate practitioner. Very few realistic scenarios involve too many back flips though.
This trope has some relationship with Imperial Stormtrooper Marksmanship Academy because the tiny but skilled fighter rarely meets a stronger but also skilled fighter, even when she's fighting cops, mercenaries, and other people who should be trained in violence.
Edith Garrud, the main bodyguard for the British suffragist movement, who learned various forms of ju-jitsu - including Bartitsu - and used that knowledge to pummel the police twice her height and triple her bulk who kept trying to break up suffragist meetings and arrest their leaders. Even made her own Badass of the Week entry.