Believe it or not, the very first JoJo of JoJo's Bizarre Adventure was not an emotionally-retard-fencepost with less tears than a cement-block (such as Kujou Jotaro); rather, Jonathan Joestar is a well mannered, sweet tempered, sensitive and kind hearted Boy Next Door and Gentle Giant who protects the innocent and openly sheds tears of compassion, even for his enemies.
Soul Eater has Maka. She's a sweet, cute, and kind young girl... who also wields a badass scythe, can hold her own against powerful enemies, and saved the whole damn world from the main villain all by herself after every other character was defeated by him (in the anime).
Shiro is all happy giggles and singing...Then something pisses her off and she dropkicks giant robots and blows up buildings. Worst of all, she'll eat all your snacks.
Ganta is a little fourteen year old boy with big grey eyes and is just really damn adorable◊- and to top it off, he's a huge woobie, especially in the first episode. Now watch what happens when the Red Man is mentioned.
Mavis, the first Guild Master of Fairy Tail, who manages to be kind, cute, mysterious and hilarious at the same time, and badass enough to master and cast one of the most powerful protection spells in the Fairy Tail universe, Fairy Sphere, from beyond the grave. On top of that she created and can probably cast Fairy Glitter and Fairy Law. Mavis only proves herself more of a Badass when she provides Team Fairy Tail with a strategy so she could lead them to victory, and she developed said strategy by memorizing and analyzing their opponents the entire Grand Magic Tournament. According to Makarov, her nickname was "Fairy Tactician Mavis" because she was able to compile many victories through strategizing. Damn.
There is also the young Sky Dragon Slayer, Wendy. In her introductory arc, she's nothing more than The Medic on an allied team of three other guilds' aces, but by the time the Grand Magic Games come around, she has grown into a certified Combat Medic capable of standing side by side with any of her nakama. She recently achieved Dragon Force while fighting one of the demons from the Book of Zeref by eating Anti-Magic particles surrounding a magical doomsday device.
Even Happy proves he can be just as badass as his stronger guildmates when pressed enough, as shown when he defiantly yells at Nichiya and Nadie during the Edolas arc.
Happy: WE'RE FAIRY TAIL WIZARDS, WE DON'T WORK FOR YOOOOOOUUUUU!!!
Solty Rei: Solty Revant. Cute, shy, plucky, considerate, compassionate... and a Robot Girl who will quickly make with the ass-handing to ANYONE who threatens her adoptive family.
Daisuke from D.N.Angel. And Satoshi to a lesser extent.
Major Alex Armstrong! The childish sincerity of this big teddy-bear really makes you wanna give him a big hug. Unless you're Ed, in which case you're getting glomped and begging him to "Stop rubbing your chest on me!"
Yoshika Miyafuji in Strike Witches also qualify. She is the little sister of the team, but is also the most powerful one. Specially after she regains her magic in The Movie
Shiro Kabuto from Mazinger Z and Great Mazinger. He is the cute, ten-years-old Annoying Younger Sibling of the main character. And he is also pretty Badass when he wants, beating bullies bigger than him or adult men, or even piloting the Hover Pilder (the flying device was necessary docking on the head of Mazinger-Z to start the Humongous Mecha).
Goro Makiba from UFO Robo Grendizer also counts like a cute child capable of awesome feats. At least his incarnation of the original manga. In one arc Barados kidnapped several hostages and hijacked Great Mazinger, and then tied his prisoners to the Humongous Mecha to prevent Duke from fighting. Goro managed to get rid from the ropes tying him and then released Kouji.
While he's pretty cute and tough to begin with, it's only through Character Development that Tetsunosuke becomes that much more Badass.
Also, Okita Souji. He's constantly smiling, loves candy, plays with the neighborhood kids, has a cute little piglet as a pet that he fawns over, is pretty much a male House Wife to Hijikata, and is well-known for being the most terrifying swordsman in all of Japan.
Nagakura Shinpachi, especially with Art Evolution gradually making him look more and more like a kid-edition Bishōnen. Despite appearances, he is a very competent swordsman and commander, and still inspires the urge to cuddle him even while splattered with blood.
The eponymous character of Rurouni Kenshin. It's the "oro?" The fact that he is the first genuinely sensitive, kind-hearted and nice anime bloke since Goku and Kenshiro, rather than just another emotionally repressed and cynical JerkassNineties Anti-Hero. And then you have pretty much half the cast with Kaoru, Misao, Yahiko and Soujiro all invoking various flavors of this trope.
Shinji is painfully shy, his self-esteem is screwed up but he still tries to be a Nice Guy. As for badass, anyone who says he doesn't qualify in the original series should one day just try holding red-hot pieces of metal for half a minute (never mind fighting someone in the process). Yes, his hands weren't damaged directly, but he felt all the damage to Eva-01 as if his own body was harmed. In Rebuild 2.0 - "GIVE REI BACK!" Commence reactivating 01 on willpower/rage alone, rocket punching Zeruel (or as close an Eva can get to one), saving Rei and almost ending the world. There just may be some Kabuto genes in him.
Also by Gainax, there's Nono in DieBuster . Arguably, the cutest robot you'll ever meet, is in fact the seventh Buster Machine and a Person of Mass Destruction capable of controlling the Buster Corps, slicing one of Saturn's moons in half and kicking the shit out of an Eldritch Abomination the size of a planet. And all of this while being ditzy and having Nia's voice.
A lot of Pokémon owned by characters in the anime fall under this. IE: Pikachu, Bulbasaur, Charmander, Piplup, Teddiursa, Raichu and Clefairy are just a handful of examples.
One of the most prime examples is the 1st gen Pokemon, Mew, which is ungodly adorable and is always shown to be very playful and childlike, not to mention is literally described as being the 'Psychic Kitten' Pokemon. One could hardly take it seriously until you realize that it's capable of using every single non-legendary specific move in the entire series.
In addition to actual monsters, some of the human characters also qualify. Ash Ketchum has the appearance and mannerisms of a brash, classically adorable little boy. He's also one of few humans to physically put himself on the line for Pokémon in the series, jumps around like a Mankey to rescue said Pokémon, and is even capable of using Aura. Did I mention that he risks or even knowingly sacrifices himself for Pokémon regularly? Maylene, Whitney, and Misty may also qualify; Maylene is basically described this way by other characters.
This trope also holds true for the human protagonists of the Pokémon Special manga, as nearly everyone fights alongside their Pokémon. Special mention goes to Sapphire, who at the mere age of 10 is already capable of fighting Pokémon on her own, and is apparently strong enough to rip apart fountains and sprint while carrying a fully-grown man.
Hareta from Pokémon: Diamond and Pearl Adventure is rather young but can go against Pokemon, can lift things far heavier than him (including a Rhyperior), and has a common battle strategy which can be summed up as "I fight alongside my Pokemon no matter how tough the opponent".
Shibata Taketora of Shibatora is a 22 year old police detective who's regularly mistaken for a middle schooler. His female coworkers tend to fawn over him (one of the men says that something about him seems to trigger maternal instincts,) and he's constantly refused service or even kicked out of venues under the presumption that he's a minor. He's also the current kendo champion of Japan, having become the youngest title holder while he was in police academy, and is more than capable of dispatching most foes with a handy Improvised Weapon.
Digimon Adventure has Gatomon, who is a little cat mon... who happens to be able to take down six Champion/Adult Digimon without breaking a sweat. Technically, she was a Champion level too... but she still qualifies.
Noir has Kirika-chan, who elevates the trope to BadassWoobie. The fact that she is so cuddly and huggable really helps. There's also the flashback where she commits her first assassination around the age of five! Certain death has never been so cute.
Shiki Ryougi. Mixed with a healthy amount of Fanservice, as expected of Nasu, whenever she gets all dere-dere toward Mikiya, she's extremely huggable and borders on Moe. That's, of course, when she isn't slicing up ghosts, zombies, magicians and stuff.
Also in the same series, we have Azaka Kokuto, Mikiya's younger sister who can set things on fire and kick giant flower demon thing on the head, and finally overpower aforementioned Shiki. She does that while being extremely Moe.
Son Gohan is a pint-sized child who can trash world destroying super-powered psychopaths.
Same thing goes to young Trunks and Son Goten during the Buu saga.
Son Goku, even as an adult, is an endearingly innocent and kindhearted boy... who has saved the world so many times that he has "lost count" (to be fair, he did have trouble counting past eleven due to brain damage suffered as a baby).
Nodoka Miyazaki. She interrupts a fight between Negi and the Big Bad just to gather intelligence and mind-reads and taunts the Bigger Bad. Afterwards goes back to being her humble Moe self.
Though she would threaten to kill you for calling her this Evangeline could count as well, as she has the body of a ten year old and has fondness for Elegant Gothic Lolita but has the mind of a 700 year old vampire mage.
America had Super Strength even when he was a kid, though he seems to use it more for throwing buffalo/dragging vehicles around/ripping windows off their sills than beating people up. Still badass and adorable.
The young Italy once took down Turkey. It was a onetime thing but it proved he can be badass when he wants to be.
Russia is pretty badass and scary and has tons of fangirls in Real Life that think he's the most adorable thing ever.
Allen from D.Gray-Man: exceedingly adorable. But, since he's a shonen protagonist, he's also made of Bad Ass. Anyone who can shout the name of his Innocence (Crown Clown) without looking like a total idiot automatically qualifies.
Tony Tony Chopper is an adorable little reindeer kid, who nonetheless can turn into a muscular fighter and be quite badass when the situation requires it. That's not even going into his monstrous Deadly Upgrade.
Chapter 731 introduces (or rather, reintroduces) Koala. Last time we saw her, she was a little girl who Fisher Tiger had brought home after she was freed from slavery. Now, she is a young woman, a member of the Revolutionary army, and a substitute teacher of Fishman Karate, a fighting style previously thought to be exclusive to Fishmen. Not only that, but she was seen sitting on a few mooks she had just knocked out offscreen. And despite all that, she's every bit as cute as she was as a child.
Nel Tu in her adult form. She takes down an opponent stronger than Grimmjow, or at least had him one strike from death before her power gave out and she reverted to her child form. Also doubles as a Crouching Moron, Hidden Badass.
Also, Rukia. Short, flat chested and skinny, with pixieish features and big eyes even by anime standards, loves bunnies, can't draw but insists on doing so anyway, has a Dark and Troubled Past, and kicks ass. Well, most of the time.
Ururu Tsumugiya, a cute young girl who assists Urahara. She appears meek, but can pack a super-power punch. Ururu is short, shy, clumsy at times, and sad-eyed... and can kick an Arrancar's ass with ease. And that's before she pulls out the rocket launcher.
Retsu Unohana. She's the extremely gentle, ladylike, and motherly captain of the 4th Squad. Despite her calm and motherly outlook, Unohana happens to be one of the oldest Captains in the Gotei 13 and has been around presumably since the beginning of the formation of the Gotei 13, and has led her squad ever since. Not only that, she hides an extremely scary Battle Aura that makes even the most Badass Shinigami go weak in the knees when imagining her wrath. This is even more evident whenever other squads start bullying her squad, whereas a slight glare is enough to send the bullies pissing their pants. Then there's subversion: when she reveals her common past with Zaraki and fights him, she is not adorable. More like an Ax-CrazyStringy-Haired Ghost Girl who is equal parts badass, scary, and hot.
We also have Orihime when she's fighting against Numb Chandelier, when she activates her Shiten Koshun against Ginjo, and when she stands alongside her friends to fight more hollows.
Hardly your usual example, but Ukitake is rathersweet and like Unohana is one of the older captains. When he teams up with Kyoraku to fight Starrk that mild-mannered niceness suddenly looks a lot less harmless; "Did that guy just fire a cero?"
Also, Hiyori. She appears as a tomboyish, cute little girl, with a rather violent temper, and she isn't afraid to make this violent temper known to her enemies.
And her companion Mashiro, a Genius Ditz who dresses up as a Kamen Rider fangirl and can kick just as much as the original does. She literally does kick ass, "RIDER KICK!"
Yachiru. She's small, cute, gives nicknames to everyone, and rides around on the shoulder of everyone's favourite badass, "Kenny." She's also the lieutenant of the combat based squad 11 for good reason, and the only reason she never gets to show off is because she likes letting Kenpachi enjoy his fights. In fact, it's been hinted that she's actually stronger than him. Also, she has pink hair.
Julian Mintz from Legend of the Galactic Heroes: starts the series as a little-boy Bishōnen, end it as a blond haired pretty boy. You would never suspect the things he can do with an axe, ESPECIALLY if you push his berserk button (like killing seven guys passing by in fourteen seconds, scary...)
Yu-Gi-Oh! GX: Marufuji Shou. Short, cute, adorable beyond words. Juudai's the hero, but Shou is badass. And he does it all wearing glasses, too.
Yu-Gi-Oh!: Yugi Mutou himself. Not only is he short and incredibly adorable, he's super special awesome enough at Duel Monsters to defeat his super sexy ancient Egyptian alter ego. To top it off, he's voiced by DAN GREEN in the dub.
As of chapter 57, it seems Elizabeth is one too. She desperately wanted for her fiancé Ciel to not see her "uncute" side, so she deliberately hid her badass side. Right up until when Ciel despite his best efforts ends up injured and unable to save her in danger himself, then Elizabeth leaps into the air and takes down the zombies with swords in both hands while tearfully declaring that she'll protect him. She fights, still in her adorable dress with a cute but deadly expression across her face.
Mariko from Elfen Lied. She pulls off both terrifying and adorable.
And Lucy? Her Nyu persona is the epitome of cuteness but she can also be adorable herself, for a murderous Yandere.
Shion also counts. She's adorable for a seventeen year old, and can be pretty awesome(andscary). Rika also counts when she becomes a determinator.
The adorable Woobie-riffic Satoko. While she may not seem badass at first there's no denying the awesomeness in her finally calling her abusive uncle out and yelling at him to "GET OUT!" despite being beaten while doing so. And in Meakashi-hen, she absolutely refuses to cry as Shion tortures her to death, claiming that she's realized how much of a burden she was on Satoshi and not wanting to be The Load anymore.
Keiichi. He's a Hot Blooded Bishōnen who can be adorable and hilarious at times and at various points demonstrates epic displays of GAR-ness.
Hunny-sempai from Ouran High School Host Club: while adorable, small, blonde, and cake loving, Hunny-sempai is also an expert martial artist and was able to single handedly take out 7 professionally trained and armed men in 15 seconds flat without so much as breaking a sweat. To top it all off, he scolds the by wagging his finger at them and saying that "hurting my friends is a no-no".
He also beat the crap out of 2 platoons of green berets after one of them woke him up from a nap. Hunny-sempai is not a morning person...
Also, after beating the crap out of his dad (who was supposedly the strongest martial artist of their family), the Japanese Secretary of Defense, who was the referee, begged Hunny-sempai not to fight in public ever again, lest other countries think Japan was training a WMD...
Akise Aru. Much like Yukiteru he's very cute. He's also undeniably badass. There's no doubt about his badass status when in chapter 51 despite having just been stabbed by Yuno and sliced across the throat, Akise Aru gets back up out of sheer determination and texts an important message to Yukiteru even though Yuno ends up cutting off his head completely. Badass to the end.
Sweet, innocent, adorable little Astro of Astro Boy fame is one of the cutest things on the planet - and equipped with mountain-levelling strength before you get into his absurd amount of onboard weaponry. Actually, Astro might be said to have created this trope.
In the 2009 film, he defeats a colosseum's worth of robots made to kill other robots and is merely out of breath; in the final showdown, he flips Peacekeeper over his head after it's absorbed the military and half of Metro City, and is then able to slow the city's fall after the generators blow out.
Guchuko from Potemayo. Looks like a plushie, has the personality of a stray cat, carries a scythe, and can shoot laser beams at anyone who annoys her.
Utawarerumono's Aruru takes out a small group of soldiers using a tiger! (Granted, the tiger isn't part of her physically, but it might as well be) Did I mention that she is cute enough ''that the Big Bad (at least, part of him) brings her back to life twice!
Gon from Hunter × Hunter. Gon is very much a BishōnenFriend to All Living ThingsCheerful Child. His first shown action is ripping a fish that's about five times his mass out of the water by main force and then carrying it back to town over his head. At a dead run. Some time later, he proceeds to break the arm of a superhuman assassin... by grabbing his wrist. With one hand. Why only one hand? It was courtesy of his other hand being inoperative because Gon got his arm broken the day before after an absolutely brutal Determinator sequence where it was shown why twelve-year-old boys rarely win fights with top-flight adult ninja.
Killua, on the other hand... is also a kid-Bishōnen. In his case, though, he knows it, and has more-or-less weaponized it... so that he can get closer to his targets, as he's been trained as one of the world's deadliest assassins pretty much since he could walk. And given that this is a world where Training from Hell and Charles Atlas Superpowers actually work... yeah.
Seras Victoria from Hellsing. She's very much a MoeWoobie, but swings around a massiveBFG, and after she drinks Bernadotte's blood she becomes the second strongest vampire. Her absolutely epicCurb Stomping of Zorin Blitz, shortly after Zorin Mind Raped and mutilated her, and killed Bernadotte deserves mention.
Nina Liebert from Monster is a deconstruction. She's a beautiful and kind-hearted Woobie who undergoes a Break the Cutie process repeatedly and yet she goes from being an ever-so-wholesome law student to a worldly, hooker-impersonating, gangster-frightening gunslinger in about one volume, and mostly through her own efforts. However, despite having the skills and the adorable looks, we see that the poor woman has borne a MASSIVE Trauma Conga Line ever since she was a little girl, so her mental fortitude simply can't keep up and at some point she has to be talked out of committing suicide when she realizes how utterly horrible her life has truly been. Just being Badass And Adorable will NOT cut it.
The eponymous Sailor Moon. And Chibi-Usa. And Ami. And Chibi Chibi. In fact, most of the girls in the series count because most of them are sailor soldiers.
Yuki Sohma of Fruits Basket. Incredibly Bishōnen, polite and a real sweetheart, turns into an adorable rat when hugged by the opposite sex, and he's also capable of beating the crap out of his cousin Kyou whenever they have one of their duels.
Kagura Sohma. She's adorable and is incredibly capable of beating the crap out of Kyou. Check it out here.
Kyou himself qualifies, especially early in the series before all the boys have a rather impressive growth spurt. Troubled, but Cute, turns into a cute cat when hugged by the opposite sex... and despite being the family punching bag, Kyou is a formidable martial artist in his own right, and has done enough damage to Shigure's house to prove it. His first entrance consists of smashing his way down through a roof to challenge Yuki to a fight.
Also, Mikado, the shy, gentle Ordinary High-School Student who's new to the city. He also has managed to more or less weaponize Anonymous by being the leader of a massive organized gang called the Dollars that he directs via cellphone texts and chatrooms.
Anri is a competent sword wielder (of Saika, nonetheless) and has proven to hold her own in trouble.
Alice of Pandora Hearts. She appears as an adorable hot-headed little girl. She is actually the infamous B-Rabbit (Bloodstained Black Rabbit), the strongest chain in the Abyss.
Oz is also this, when using Alice's power on his own, even when still under seal.Then, it turns out that HE is B-Rabbit in Jack's body and his powers bound to Alice's soul.
Lily is one of the Baskervilles. She looks right about ten.
AdorkableBookworm Leo becomes thiswhen it turns out that he is Glen Baskerville, the leader of those Baskervilles, and is currently contracted to Jabberwock.
L. He's a Badass Bookworm and the greatest detective in the Death Note world. He also has a large amount of fangirls who all agree that he's rather adorable, and he has bizarre child-like mannerisms.
Also, Near. More maternal members of the audience may want to hug him even as he manipulates everyone around him.
Light Yagami himself has his moments of badass adorable, especially when he's younger. In some of the artwork, he looks like a Disney character while contemplating murder. Special mention, however, goes to the time when he loses his memory and reverts to his original good personality; some of those scenes portray him as absolutely huggable.
Teru Mikami deserves mention, as a child. Going up against vicious bullies despite getting beaten up again and again, all in the defense of a fellow classmate? Badass.
Momo from Peach Girl. She's pretty and has huge eyes. Really, she's a really sweet girl so long as you don't rouse her temper. If you do happen to piss her off...you may very well get a foot to the face, a headbutt, or a knee to the groin for your trouble. Her crowning moment came when she single-handedly beat up a huge guy who was trying to rape Sae. Other than that she's just a misunderstood girl trying to find true love.
Ranma's girl form is adorable, and he often uses it to score free eats. His male form is handsome, but not adorably cute. Regardless, mess with him and he will find a way to pound you into the ground -smaller female form notwithstanding.
Shampoo has the implied willingness to rip off somebody's head and spit down their neck if ticked off. She also very pretty and sweet-looking.
Kaiji grows from a shrimp into a pretty competent fighter who acknowledges his weaknesses. Some will argue that the whole point of this series is to see Kaiji lose tremendously, get back up in an inspiring and heart-winning manner...then lose even more tremendously. In the end, you just want to give him a hug or buy him some drinks after all that's happened to him (losing scads of money, betrayal and bullying, maiming, losing his comrades, being forced into slave labor, being harassed by a girl he doesn't like...the list goes on). Many, fangirls and fanboys alike, will argue that Kaiji is indeed "moe", or moeGAR.
Kagura of Gintama. Her quirky, childish tendencies are all so endearing, but she can hold her own against an entire army if need be.
Simon of Tengen Toppa Gurren Lagann, who takes the level of cuteness possible for a Badass Adorable to rather impressive heights. He's basically an endearing and initially-timid cutie who also happens to be one of the strongest, if not the strongest, Spiral warrior in the cosmos (his Big Brother Mentor Kamina initially exceeded him merely due to his charisma and courage). Later in life, after progressing to Bishōnen he manages to summon a mecha the size of a galaxy and save the sentient races of the universe from extinction at the hands of a sociopathic despot. Even then, he still retains his optimistic and endearing personality. Manlymoe, literally, doesn't begin to cover it.
The Child. It's largely speculated that the once misshapen fetusthat was Guts and Casca's tainted child caused by Griffith's very heinous act during the Eclipse has been reborn into the very cute and silent little boy that Casca found on the beach. And if the implications are correct, the little boy is still doing what he was doing when he was not-so-cute: warding off evil spirits that try to harm Casca. But the true badass part comes when Guts is overpowered by the Beast, who constantly tries to goad him into killing Casca and all of his friends so he can get back to hunting Griffith. But whenever the Child is nearby, the Beast is always thwarted when the the boy manifests as a body of light within Guts' psyche and brings him back to the light by reminding him of his lovefor Casca.
Guts was pretty cute as a Child Soldier himself, and he could hold his own ground on the battlefield.
Momoka Oginome in Mawaru-Penguindrum. A young girl no older than 10 who is capable of rewriting reality via writing spells in her Destiny Diary at great risk to herself, and who had done a LOT to save two other children who badly needed her help.
Unico, an adorable baby unicorn who has the power to bring happiness to whoever he befriends, but is also able to fight against enemies, and is capable of growing to a giant adult sized winged unicorn as necessary? Bonus points since, like Astro Boy and Kimba, he was created by Osamu Tezuka.
Kirby is a pink ball of kindness and will swallow you whole and steal your powers.
Fumu, too. She's the cute little Cappy girl who cares for Kirby and usually tries to end conflicts without employing violence. But in the second Dedede Elementary School episode, she takes a level in badass and singlehandedly beats up large armed thugs without even touching them.
From Tenchi Muyo!, we have Sasami. Adorable, pre-teen princess, darn good cook, most down-to-earth member of the entire cast that wasn't born on said planet. Depending on the series: she has a hairband that turns into a staff for serious Waif-Fu action, can use Juraian magic on par with anyone else, can summon a mini-mecha battle suit, oh and she just happens to be the incarnation/host of one of the three 8th-dimensional goddesses that created the universe as we know it, as little more than a science experiment.
Nogizaka Haruka no Himitsu: Nogizaka Haruka rarely shows the badass part of the trope but the first time Ayase Yuto saw her doing it was enough to make him understand he must never make her angry. And that's because her anger was directed at a boy trying to take her from him.
Naoya from Lotte no Omocha. He's shown to be able to effortlessly throw Sigurd — a Warrior Prince with a lifetime of military training — aside using the momentum of his flying headbutt, implying skill in either Aikido or Judo. This is further justified by a photo of him that Lotte happened upon in his album, of him in a gi (Japanese Martial Arts Uniform) with a green belt, but four steps away from a black belt, as a child.
Gerda, from the animated adaptation of The Snow Queen. She is a 11-years old Danish Genki Girl that can take on boys much bigger than her (she apologizes, though), she is the one that persuades the others to go to a forest nobody went before and, when her best friend is taken by The Snow Queen, she goes in a journey to find him, alone, and the stunts she can pull in the journey, few people can.
In The Doraemons Special series, all of the robot cats can count. Especially Wangdora and Dora-the-Kid.
While the "badass" part is something in the own heads, Rikka and Sanae from Chuunibyou Demo Koi ga Shitai! could still count, as they both fit firmly into the "adorable" part.
The Mahjong anime Saki has three examples. Saki herself easily qualifies giving her shy andquiet personality as well as her woobie status. Koromo also definitely qualifies given her small and cute appearance. Nodoka could also qualify as well. All three of them are adorable and all three are plenty badass.
KamikiIzumo also counts, for those who prefer Tsundere characters. She summons cute foxes to fight for her, who can summon smaller, even cuter fox kits who are also quite tough. Not to mention gets adorably flustered when people (especially Rin) are nice to her and secretly likes cute things. Her Dark and Troubled Past that has been revealed recently has sent her into The Woobie territory as well.
Kirito himself counts - the Kid saved the world twice, and after a year of being trapped in the online world, was one of the highest-leveled players in the game. And he looks...kinda girlish and is very sweet.
Yomiko Readman from Read or Die. She's a kind of spacey, hugely nerdy bibliomaniac who always uses extremely polite language, and treasures books above almost anything else in the world. She is also fully willing and capable of taking down armed, powerful men with sheets of paper.
Amamiya from Psyren. She's the very definition of Action Girl, but anytime she's having a moment with Ageha or fangirling over Matsuri, her Moe side comes out.
Any of the Tenjuin kids during the present day are not only cute, adorable, and over the top, they are some highly accomplished and powerful Psionists. Special mention goes to Mari, who not only becomes one of the most gorgeous girls of the entire cast, but becomes even more powerful and adorkable in the future
When not in self-doubt, Izumiko from RDG: Red Data Girl can be quite a badass while remaining cute (and not just when Himegami takes over).
Sweet, bubbly Hajime Ichinose of Gatchaman Crowds has proven herself to be a competent heroine. Holding off Sugane, and convincing MESS to stop their attacks and free the humans was just the start.
Sweet lord, Kuro from Kurokami. Short, sweet, and adorable as hell, Kuro can tank more damage than most adults, which is especially notable given that she can tank and dole out more damage than many of the other characters in the series a significant portion of whom are superpowered beings unto themselves. Given her Tragic Past, you just wanna hug her that much more.
In Space Dandy, Adélie the Gentooan orphan looks like a sweet, young, harmless Humanoid Alien. The reality of it is that she's been alone and hunted by Alien Registers for quite some time, so she's very good at fighting them off. Her standard operating procedure is to immobilize them with her stingers, then trap their minds inside stuffed toys and leave them.