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.
While Harry shoots up height wise to the point where he's about five foot nine by Easter (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.
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 he’d 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.