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.
Natasha isn't particularly short for a woman, but compared to most of her team mates, she's pretty small. She's also the one who people routinely find the most terrifying.
Bruce and Tony are technical cases - they're fairly small men, but one armours up and the other transforms into a rage monster to become combat effective.
Karrin Murphy of The Dresden Files makes a fairly brief appearance, but in that brief appearance the narration notes that Coulson treats her with the same kind of respect he would give to the Black Widow, because he knows her reputation.
Diana is a Cute Bruiser who plays this trope straight as an arrow until a (temporary) Plot-Relevant Age-Up turned her into a Statuesque Stunner and amped her already considerable Super Strength to Thor levels. Thereafter, she hits a growth spurt, meaning that she's around the upper end of this trope by the second book.
While Harry shoots up height wise in the first book to the point where he's about five foot nine by Easter of his 3rd year (shorter than average to average for a grown man, tall for his age), but he's still routinely facing things much larger than him. Unfortunately for them, like another wizard called Harry he's something of a prodigy with fire...
The fic Mortality has this with Mary, and Watson, since in the fic "A Study In Regret" they get killed but this plays it straight with Watson since he calmly killed Culverton Smith and most likely with his medical skills.Yikes.
In Flashpoint 2: Advent Solaris, most of the Sonic characters serve as this in comparison to the DC characters as most of them are stated as being merely 4 feet tall - the size of human children & teens compared to the DC cast of mostly grown adult humans. Most apparent with Shadow, the utlimate lifeform, who practically personifies this trope in the fic.
Ringo in With Strings Attached. Granted, he's not that short (5'8), but at one point, when he had been travelling 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.
Red Fire, Red Planet has Meromi Riyal, the Orion first officer of the IKS mupwI'. She's barely 147 centimeters tall (a bit less than 4'10") and weighs 43 kilos (95 pounds). When Norigom, the Nausicaan ops officer, propositioned her, he came to half an hour later "with four cracked ribs, two broken metatarsals and a nose that was somewhat flatter than it had been when hed entered the room." He's been herHopeless Suitorever since. A later chapter states that, being so small, Meromi relies on martial arts moves that favor finesse and leverage over brute force.
Though we never get to see it fight, the Optrican starship OAV Watchkeeper in "Aen'rhien Vailiuri". It's about the size of a Defiant-class and is said to have six weapons emplacements equivalent to the main gun of a Jem'Hadar attack ship, and shields comparable to an Ambassador-class. It's a little outdated compared to the Romulan characters' D'deridex-class but they're impressed nonetheless.
Even using Element Zero to double their canonical size, the Sword of the Stars factions in the crossover story Shepherd Of The Stars still use ships that are half the length of their Mass Effect counterparts. Despite the size difference, the Sword of the Stars ships carry enough guns to equal and occasionally surpass the armament of Council vessels. A great deal of time is put into explaining why they are able to do this and how Council ships are able to still be competitive with such tiny monsters.
In the fanfic Sugar Plums the protagonist Ume is absolutely tiny especially compared to everyone else around her. Not only is she three years younger than her graduating class (she joined the academy at five instead of eight) she is much shorter than most people her age. At twelve years old she's only 4'3 inches (a full half a foot shorter than Naruto is the shortest member of his graduating class), but she's also a fully trained shinobi and a physical fighter.
In Neither a Bird nor a Plane, it's Deku!, Izuku is a fairly short 5'5'', significantly shorter than several of his male classmates and a full foot shorter than Mercy, Lexi Luthor's bodyguard. But Izuku is also a Kryptonian and in the running for the strongest freshman at U.A. and is the only applicant at Testing Facility B strong enough to take on the robot Starro replica.
This is ShadowClan's shtick in Warriors Redux. They're scrawny looking and small but are known for being vicious in battle.
The Pokémon Squad: June, just like on her home show, is a good example. In the episode "Elmo Knows Where You Live", she's strong enough to break a cinder block wall with nothing but her fists.
Us and Them: Aeris and Sephiroth's second child Remi is strong enough at age three to actually cause Seph pain. This, combined with her ferocious temper, causes Aeris some serious worry about her hurting someone, accidentally or otherwise. Eventually, she and Seph decide to have her start training with the staff to both give her an outlet and teach her discipline.
Missy Coco, Callista's dark-minded child double in Zero Context: Taking Out the Trash. She possesses enough magical power to casually one-shot entire neighborhoods and be taken seriously as an enemy by the Goddess of Nature. The author's notes for the story clarified that Ai Haibara was used as her physical basis when he created her, meaning that she's not that much taller than the average six or seven-year old.