Hyraxx D'Mofiti from Buck Godot: Zap Gun for Hire is an alien who, while not all that small, is about a head shorter than average humans and is of fairly slight build. Yet she is able to throw Buck, who is several times her size, around with ease an collapse a heavy wall on him. Buck assumes she's another assassin sent after him but actually she's just a tabloid reporter (although in the setting being able to not get killed is more important than being able to make a good story if you want to be a successful journalist).
Basically any Racconan in Tales of the Questor. They top out at around two and a half feet tall, but their "magic" powers, martial traditions, and sheer love of overkill make them a hazardous handful.
Da'kor from Inverloch. They are the size of a human child, but in a fight an unarmed da'kor has a fair chance of defeating a human swordsman.
Nike from Demon Eater. Sure, he's larger than the main character, but there are true gargantuans out there. And none can stand a chance against him.
Song from Tales of a Gay Asian she is less than 5'7 yet she can easily push 3 sophomore boys into a wall.
Ixnay from Elf Blood: She's a pixie, literally around as tall as a pint glass. She's not strong enough to operate human/elf-sized door handles. She can easily take down a seven-foot tall, armoured hulking brute in a fight through guile and magic.
In Schlock Mercenary, the titular mercenary ends up eating a plasma grenade, which destroys most of his body mass. Being a carbosilicate amorph, Schlock's distributed body system meant that he survived, but as a much smaller version with child-like innocence and little memory of his past. But though he's only about the size of a human head, don't mistake him for being any less dangerous, as he managed to shoot down a cruiser when he got loose inside it.
A power of one of the heirs in Archipelago. Though she isn't actually short herself, the power she has enables her to shrink, and get proportionally stronger and tougher; which, among other things, has enabled her to punch through stone golems and surviving tons of falling rocks.
Nanase of El Goonish Shive is only about 5'4", but is widely regarded as possibly THE most skilled fighter among the main cast. She can also bench press up to 160 pounds (almost certainly more than Nanase herself weighs), and that's without her magic passively enhancing her strength; WITH magic, she can bench over 200.
Bad Moon Rising has Madison, who stands just about five feet tall and picks fights in bars full of dangerous hunters of supernatural beings — none of whom have any reason to like her, given that she's technically supernatural herself — for fun. Even smaller is her brother Peter, who is introduced lobbing Molotov cocktails at vampires, but his status is debatable: Peter would probably be of average height if he had legs.
Mario & Luigi: Cleanup Crew: Toad is not only able to carry Toadette while running at full speed, he's able to carry Princess Peach carrying Toadette.