There have been several child characters who've qualified: young Goku and Krillin, as well as Chaiotzu in the original series, young Gohan, Goten, Trunks, Gotenks, Uub and Pan in Z, and Goku again in GT.
Outside of kids, some other powerful characters have been on the small side as well: adult Krillin, Guldo, Android 15 and the Cell Juniors being some of the shortest.
Vegeta isn't unnaturally short, but there's still a definite difference in height◊ between him and the average-sized Goku. This is lampshaded during the Saiyan Saga when Vegeta is accompanied by Nappa, a mountain of muscle who completely towers over Vegeta and nearly destroys all the Z-fighters single-handedly until Goku shows up. Between the two Vegeta turns out to be by far the stronger one, and easily kills Nappa himself as punishment for his failure (admittedly Nappa was already weakened from his fight with Goku, but it's doubtful if he really had a chance against Vegeta even if he weren't).
Kid Buu definitely stands out when it comes to this trope- he's one of the strongest enemies in the original series, able to blow up planets like it's nothing, and he's about two heads shorter than Goku.
The immensely powerful Vegito becomes one for a short while after getting turned into a tiny piece of candy by Super Buu. He retains consciousness, along with his power, and actually becomes more of a problem for Buu because he's so hard to hit.
Genki in Monster Rancher he is just 11 years old but can lift and carry older girls and women like dolls. For example cradling them in his arms, taking piggyback or by hoisting them over his shoulder, mostly by running away from monsters and protecting the "helpless girls".
Kenshin Himura in Rurouni Kenshin, aka the Hitokiri Battousai, is towered over by most of his friends but routinely takes down people twice his size. He's based on a real life assassin named Kawakami Gensai, who was regularly mistaken for a woman, but who was known as the most fearsome assassin of the Meiji Era and was noted for assassinating a man in broad daylight. Kenshin is also a subversion of sorts - because his school of swordsmanship was designed for far more muscular men (like Hiko, his Cynical Mentor) he ends up unable to fight as well as he once could at the end of the series.
Yahiko's an extremely straight example, taking on minibosses regularly after the Kyoto arc, especially after he learns the Kamiya Kasshin-Ryu Succession Techniques.
Ash's Pikachu in Pokémon. It can also be quite scary in the games when equipped with a Light Ball.
A good deal of the team's main Pokémon tend to be this (and if they're lucky, will kick the butts of their evolved forms down the line!). Of course, there's the sheer irony in Brock's Happiny being one of the physically strongest when the games have its physical Attack with the likes of Shuckle and its evolution Chansey. Misty's Psyduck can often be the most powerful member of her team if it has a headache.
Then there's Croagunk, whose testament to battle was shown in the first DP movie when he easily blocks a Draco Meteor fired by a Legendary Pokémon!
In the first movie, Mew, a cute little guy, was able to fight his evil, intimidating clone Mewtwo to a standstill. (A clear example of Artistic License; in the game, Mew wouldn't stand a chance in a fight between the two.)
Sagara Sousuke from Full Metal Panic! against pretty much all of his major enemies / rivals. Every single guy he has a serious fight with is built much larger than him, is older, and has a whole lot more muscle than him. However, he holds his own very well, and pretty much always wins in the end.
The president of the Karate Club in Fumoffu seems to be even better in the martial skills, being the same age and size as Sousuke. His casually defeats multiple opponents, each one much bigger than him and sent Sousuke to the ground withouthis glasses
Astro Boy, the original pint-sized powerhouse of anime.
Claymore has Miata, a single digit who looks and acts like a little kid and is smaller than most of the other Claymores, but can kill yoma with her bare hands. The Organisation's men speculate that were she not mentally unstable and needing Clarice's constant care, she could easily be a Number 1.
Negi of Mahou Sensei Negima!. Not only is he a kid capable of clearing out an arena filled with huge men using mostly martial arts, but even in his adult teen form, he was still smaller than most of the people he fought and beat the crap out of in the Magic World Tournament Arc and gave the towering Game BreakerJack Rakan the fight of his life.
Evangeline as well. She's so incredibly powerful that there are perhaps five people in the world capable of putting up a decent fight against her... not that you'd ever guess it, due to her having a perpetually 10-year-old body.
Also Kotaro and Yue.
A certain amount of Fridge Brilliance sets in when you realize that Negi learned his martial arts from Ku Fei, herself a Pint-Sized Powerhouse. Due to her small stature and petite frame, Master Ku would naturally know plenty of techniques designed to fight larger opponents.
Hiei. 4'9 without his hair and can beat up guys twice or three times his size with ease (and when introduced was much weaker than when he was a child). Kurama may also qualify- he's not short, but he's pretty skinny.
Guys. Genkai. She's barely taller then Hiei. In her first episode, she knocks two rude and huge men into a wall just by shouting a wave of energy at them. And complains she's getting old, and in her youth she would have obtained the same result by looking at them. Be polite to your elders.
And some of the guys from the various tournaments. But with the exception of Genkai they're all demons.
InuYasha: Shippou is both a child and a kitsune. As a result, he is tiny, much smaller than even children of an equivalent age. Despite having no time to prepare for a set of exams he didn't even know existed, Shippou thrashed his fellow kitsune, achieving unheard of success by climbing several ranks of power within the space of a single night and going down as a legend among the other students. Although he can pale by comparison to the adults in his group, the calibre of the group he's with and the enemies they fight have ensured he's incredibly powerful by Kitsune standards.
The title character of Desert Punk is a very short guy who is still capable of wielding a high-caliber shotgun with ease, and even without it he can pretty easily beat the crap out of most people. Of course, he's later outclassed by Mitsuru, who's like 11, but if you piss him off his "Hulk Syndrome" lets him lift large boulders with one hand and smash robots built with Lost Technology (slightly subverted in that it may also turn him into a giant, but he's superhumanly strong either way).
And the Acrobalenos are a group of seven babies...who can kick any of the main character's ass to hell and back.
Yugi Mutou, from Yu-Gi-Oh!. Granted he does have an extremely powerful alter ego in his head but the final episode of the series proved that he could kick his ass as well, in the most epic duel of the series.
Daikichi Komusubi of the Deimon Devilbats is 4'11. And a lineman. He's regularly holding off, or even pushing back, larger, more intimidating players, and speaks/writes in a language known as "Power-Go", which only 'truly strong men' can comprehend.
Luffy from One Piece is one of the shorter male humans in the series and can kick the ass of people many times his height and size and do things he damn sure shouldn't be able to do with his inhuman strength alone. In real life his height is about average (172 cm), there are just a lot of big mofos walking around the One Piece world (and that's not even counting the giants) so he just is short in comparison.
Blame! has a weapon example. Gravitaional Beam Emitter is some of the smallest weapon in the series and really small even in today's standard. The firepower, on the other hand, can putDivine Busterto shame.
The Power Card in Cardcaptor Sakura. This card spirit takes the form of a fluffy-looking, pink-clad little girl. (Who can't be any more than 3 feet tall.) But she has the strength of several grown men, and proves to be an immense challenge to Sakura.
Heero Yuy of Mobile Suit Gundam Wing was raised from a young age as an assassin, weapons expert, and robot pilot; when he participates in the events of the anime, he's 15 years old, 5-foot-1, and 99 lbs. Wu Fei also qualifies, having pretty much the exact same physical stats as Heero and being a talented martial artist.
Hunter × Hunter has its own share of insanely able kids. Killua was an assassin ever since he was born, and can extract the heart soundlessly out of an opponent, with just his hands, and he's twelve years old.
Digimon Adventure gives us Gatomon — a Champion-level Digimon with the size and appearence of a Rookie. Subverted in Digimon Adventure 02, in which she's reduced to Rookie-level strength by the loss of the ring on her tail.
Monster of the Week Thundermon is actually called this word-for-word by Digmon. He's about the size of a softball, but packs enough electricity to send any of the gang's most powerful forms (at the time. We're well away from the DNA stuff.) flying. If not for the reformed Ken and Wormmon/Stingmon, they'd have been in serious trouble.
While Skull Satamon is not as tiny as most of these teddy-bear-and-smaller figures, he is this compared to the team, since the Champion-levels and above are usually huge. We're talking a bad guy who's twice the size of a human vs. a team of colorful Kaiju. This makes it a sight to see when he hands a Curb-Stomp Battle to the combined might of the season one and two teams, including ''Imperialdramon.'
And now Digimon Xros Wars gives us Zamielmon, an evil digimon who's small enough to sit in someone's palm yet is strong and fast enough to give Mega level a hard time. However he's actually a gigantic Size Shifter and Lightning Bruiser.
Or for that matter, ReiIII who's equally as strong, if not stronger.
Taki of Hyakujitsu No Bara is tiny in comparison to his lover Klaus but consistently demonstrates that he is the last person you want to anger. Not only did he single-handedly beat up the group of military students who came to haze him, he has twice bested Klaus in combat (granted never very conclusively), showing he packs far more power and fighting skill than his scrawny body would suggest.
Shijima from Nabari No Ou is by far the smallest character the series. However, thanks to her Immortality, she is also one of the best fighters and even manages to take down Raikou after fighting for an entire night.
Tamaki Kawazoe is pretty much the central focus of Bamboo Blade for the fact that, despite being a first-year in high school (and a tiny girl, at that), she's easily the most competent fighter on the kendo team (since she had been trained by her father from a very young age). In one match, she sends a competitor twice her size flying with one deft strike.
The whole cast of Part 1 Naruto. The characters were 12 year old monsters, with some of them being even younger and still destroying mountains.
Ippo Makunouchi would like to have a word with you. As a featherweight (126 pounds/57 kg max usually) he regularly trains with people one or two weight classes above, and is considered small even in his own weightclass
In Tsukigasa, the short, girly-looking Azuma is capable of beating up 5 guys in a fight and leaving them with broken bones. His skill is part of why the damage is so extreme when he attacks his friend Kuroe later, cutting off his left arm in one strike.
In Saint Beast, despite looking younger and smaller than all of the other angels of his rank Gai has one of the most powerful elementals in the show and loves a good fight.
Levi in Attack on Titan is the in-universe World's Strongest Man and is one of the shorter characters (5'3"). He is easily able to slay behemoth-sized antagonists better than anyone else in the series.
Suzu in Seitokai Yakuindomo can do painful roundhouse kicks and outrun people twice her size, despite looking more like a child.
Minako Aino / Sailor Venus in Sailor Moon is a petite (5'2" or less), lithe 14-year-old who can knock out The Big Gal of her team with one kick, and that same kick has brought down youma many times her size in Codename: Sailor V. Also, she is the one to kill Beryl in the manga. In the fourth season of the 90s anime, her rage-fuelled power up was enough to break through a metal bind, transform into Sailor Venus, and fire an attack so powerful that it scares the ever-loving shit out of two members of the Quirky Mini Boss Squad. This happened after she'd been subjected to an excruciating attack that left all of the other Senshi unconscious.
Coo from Summer Days With Coo is able to outwrestle grown men and toss a girl clean across the room despite being only about 2 feet tall.