Son Goku, up until he was around eighteen or so, was maybe half the size of most of the other characters in the original manga. He introduced himself to Bulma by throwing her car. Even at adult age, he is only 5'7.
Dragon Ball Z: How about a piece of candy? Majin Buu turned Vegeto into a piece of candy to eat him, but was just as powerfuland too small to hit! Buu was forced to turn him back.
There's also Young Gohan, Young Trunks, Goten, The Saibamen, The Cell Jrs., and Kid Buu.
First form Frieza was probably the major example in Dragon Ball Z.
Vegeta. Woe betide anyone who dared to mock MajinVegeta.
What about Chiaotzu and Krillin? They were weak when compared to the protagonists but they were stronger than every common person and that included many taller than them. Even Krillin, who is 5'0, could hold his own against Freeza's seconf form.
Videl too..she's 5'1 and she can hold her own in fights.
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.
Taiga Aisaka, the Palmtop Tiger from Toradora has violence issues, but she's probably too much of a Dojikko to be seriously dangerous.
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.
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.
Jacuzzi Splot from Baccano is a pint-sized One-Man Army and a total badass...when he isn't a crying, whimpering mess in an attempt just to introduce himself.
YuYu Hakusho's 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.
And Rinku. And Shishiwakamaru can shrink. 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.
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 shortest male humans in the series and can kick the ass of people many size his height 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.
In general, One Piece averts this trope more than almost any other series, with most short and average height characters being weak bystanders, civilians and Mooks. It gets to the point that Hancock and Mihawk who are both pushing 195 cm (which would be very tall for Mihawk if he existed in real life, and extremely tall for Hancock who is a woman) are both pint-sized powerhouses among their fellow Shichibukai.
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.
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.