In Dungeon Keeper Ami Ami is a small, fifteen-year-old girl. Using keeper powers, she manages to fight on par with a horned reaper - in melee combat; a duel that amounted to a thinly-disguised public execution sponsored by a Dark God she'd angered. She won.
Ringo in With Strings Attached. Granted, he's not that short (5'8”), but at one point, when he had been traveling almost nonstop for about four days, had hardly slept at all during that time, and felt like utter shit, he was forced to enter single combat against a 7-foot muscleman with a giant flail. Three seconds later: “I think I win. Can I please go to sleep now?”
In the Black Lagoon fic Four Pirates and a...Little Lady?" Revy's little sister Rachel, who has turned up in Roanapur, is able to take on, and hold her own for quite a while, against a North Korean Special Forces operator. At thirteen.
AC/DC. Most of them are under 5'6". AC-freaking-DC.
Kyo from Dir en grey. He is one of the most powerful, diverse, and emotional vocalists in the metal genre. Not to mention his guttural growls are scary as hell. Guess how tall he is? 5 foot 1.
Dave Mackintosh, the drummer from DragonForce. He's 5' 4" and his nickname is Compact Dynamo.
Ronnie James Dio was only about 5 feet tall, but had one of the most powerful voices ever in hard rock/metal.
Mythology and Religion
David 1, Goliath 0. David is a youngster at that point in The Bible, but depictions often make him even younger. David could even be the Trope Codifier, seeing as "David and Goliath" is a common term for a fight where a little guy is able to beat up a big guy.
Thor's son Magni was the embodiment of strength. One myth states that Thor fought a giant named Hrungnir, but while Thor was victorious and killed Hrungnir, the giant's body fell on him, pinning him to the ground and leaving him helpless. After no-one else was able to so much as budge the giant's heavy corpse, Magni - who was only three days old at the time, was able to lift it off his father effortlessly.
In Greek Mythology, Heracles is rarely depicted as "pint-sized". However, he certainly was on the day he was born, and on that day, Hera made her first strike against him, sending two venomous serpents to kill him while he slept in his cradle. He simply grabbed them both and crushed them, one in each hand.
Rey Mysterio: At 5'6'' he is overshadowed by just about anyone he meets in the ring, but still often holds his own.
Taz is an example too, on a relative scale: at 5'9" and 240 lbs the average pro wrestler towered over him. Guess who was the toughest, hardest Bad Ass in all of ECW?
Midget wrestlers. There is one story of such a wrestler picking Gorilla Monsoon (who weighed 400 lbs) in a fireman's carry and carrying him around a ring.
Any gnome or halfling in Dungeons & Dragons who reaches high enough level. At 15th level, there's not much difference between human and halfling barbarians.
While both races take a hit to physical strength, gnomes are extremely durable, being able to endure exertions like dwarves and orcs. Compared to elves, they are almost indestructible.
The Kithkin in Magic: The Gathering's "Lorwyn" and "Shadowmoor" blocks are a little under four feet tall, but are incredibly tenacious in a fight. In fact, the most common "classes" for them are Knight and Soldier.
Yu-Gi-Oh! has a few monsters that qualify. One example is Injection Fairy Lily, a cute and friendly-looking nurse (albeit one holding a huge syringe). If her Effect is used, her Attack Score rises to 3,400, stronger than Blue-Eyes White Dragon.
Another example is Ultimate Baseball Kid. He looks like a ten-year-old little leaguer, but his effect grants him 1,000 extra Attack Points for every Fire-Attribute monster on the field (except himself) making him lethal in the right type of deck.
Then there's Goblin King. Despite the regal name, he's a small guy who's a Level 1 monster with zero points, but he gains 1,000 points for every Fiend on the field other than himself. If used in combination with cards like DNA Surgery and Opti-Camouflage Armor, this can be very potent.
The best example is Mokey Mokey. Being a Normal Monster, this guy at first seems even weaker than a Kuriboh. However, if the Spell Card Mokey Mokey Smackdown is used, these little guys become terrors, their Attack Scores becoming 3,000 apiece if a Fairy you control is destroyed.
Diz, in the Whateley Universe. She's a petite middle-schooler at a Superhero School full of high school bruisers. She can strike with a force of over eight tons with a fingertip. Her room looks like it was designed to hold the Incredible Hulk.
Worse than that, she can't not strike with 8 tons of force. Even if she wanted to. Her computer is built so it takes 8 tons and 1 ounce of force to press the keys, otherwise she either couldn't press them at all or would demolish them. Her code name is Diz Aster. Poor kid.
Reiko Ishida of Survival of the Fittest v4 is 4'9, which has been noted to technically make her a midget. However, she was an athlete before the island. On the island she manages to receive a fairly high body count; one death has her manage to beat a Huge Schoolgirl to death.