Borderlands 2 has Tiny Tina. She's an adorable if not-so-slightly nutty thirteen-year-old who also happens to be the most gifted demolitions expert on Pandora. Also Gaige, whose crimes are listed as "developing illegal military technology and excessive adorability."
Roll from Mega Man Powered Up and especially Tatsunoko vs. Capcom. Even though she's normally one of the sweeter characters, she is more than capable of taking out not only Dr. Wily's army of Robot Masters (Dr. Light's brainwashed Robot Masters, that is), but also the Lord of Darkness himself, Yami, WITH A BROOMSTICK OF ALL THINGS!
Rockman himself is absolutely adorable. And he's saved the world eleven times.
"Evil" Overlord is a bit fuzzy, his reasons are morally sound, the only reason it remotely comes close to fuzzy is because of who he's taking down. Either way he's a savior, its just which method he chooses.
Chun Li from Street Fighter. She may be the "strongest woman in the world", but when she wins a match she jumps up and down girlishly and shouts "yatta!"
Sakura fits as well with various stereotypical 'schoolgirl' entries, fighting in a sailor suit and having a huge crush on Ryu that she seldom bothers to hide.
Makoto is the cutest karate girl ever! Ibuki and her cute hairstyle is also heart-wrenchingly cute as well!
Whenever Elena isn't busy battling in the arena, she's even busier making and hanging out with friends.
Pit! He's cheerful and dorky, he's skilled with pretty much every kind of weapon ever, and he regularly kicks the asses of GODS.
Meracle Chamlotte from Star Ocean The Last Hope doesn't seem all that badass at first glance, being a StripperificMoe MoeCatgirl, but once you max out her Critical skill and get her some decent equipment her multi-hit killer moves become absurdly deadly; she can clear the field with a single Claws of Fury that scores something on the order of a dozen consecutive critical hits.
Several characters from the Breath of Fire games. Seriously, just about any female character qualifies. The best example, though, is probably Peco from the third game who, despite looking like an anthropomorphic onion, can become possibly the most overpowered character in the series if you train him right.
Bomberman with his cute face and outfit, and oh did we mention BOMBS.
Micah, the main character from Rune Factory 3, is a half-human, half-monster hybrid, and has the ability to transform between a human and monster form. Of course, his monster form is that of an adorable, fluffy sheep-like creature called a Wooly, and looks like this.◊ The "badass" part comes in when he defeats countless giant monsters in that form with his bear paws.
Grown-up Luigi is more badass than you'd think. And many fangirls consider him adorable.
Also, the various assistants from Paper Mario - Bombette, Goombario, Bow and, of course, Watt.
Yoshi. The adorable dinosaur that can swallow anything whole, turn said anything into eggs, and THEN use them as ammo. He took on a super-sized Baby Bowser while at the exact same time keeping a baby on his back and running an obstacle course, all the while trying to keep the baby from being kidnapped!
Every character in Inazuma Eleven, some of whom can and have stop flaming soccer balls with their bare hands and/or legs and have preformed kickass shots after major level grinding. Oh, and they're all in junior high, with most of the main cast putting regular Shotas to shame.
And they're successors in GO!, who can summon Kenshin; giant avatars capable of wiping the soccer field with you in one fell swoop.
And lets not forget most of the cast of the Danball Senki series, which was produced by the same company. Little kids controlling tiny robots that can be armed to the teeth with any and every weapon known to man, including BFSs, BFGs, spears, rifles, bladed knuckles, bombs, and CHAINSAWS to preform badass finishers that, in reality, would turn your living room into the embodiment of a war-zone. make of that as you will.
Said robots have also been used in the game's anime to preform and prevent kidnappings, (attempted) assassinations, professional hacking jobs, robberies, and a worldwide terrorist plot. Again, make of it as you will.
Taokaka from BlazBlue may not look adorable, and she can be pretty deadly in combat, but just the way she talks and acts in her story mode in a game full of psychos, monsters, and jaded veterans, is just too damn cute.
Keeps the badass adorable tradition going with Riki. One of the battle quotes of this Adorkable "fur ball" is "Riki can win by himself!". And he's not all talk. Far from it!
LittleBigPlanet's Sackboy. Powers of a god. Time manipulation, matter control, creation and destruction, and immortality (If you're playing the level editor). And as Yahtzee put it, he "looks like the result of a sinister experiment to concentrate cuteness to a weaponized level for use against angry girlfriends".
Soul Nomad & the World Eaters packs a few, being one of Nippin Ichi's more serious titles. You have Danette, cute, ditzy and slightly amnesiac who tears through enemies with knives and regularily makes remarks about snapping peoples' necks (and actually does so to one of your allies). Trish, a refined merchant's daughter, always positive and cheerful, who leads a mercenary company. And then there are the angels. Cute little baby-like guys... armed with guns.
Nippon Ichi also brought us Marona, of Phantom Brave fame: thirteen-year old orphan who just wants to be happy and make friends. Is also a mercenary-for-hire with an army of phantoms, routinely hired to go into some of the most inhospitable places in Ivoire to deal with supernatural threats and attacking armies, managed to slay a legendary monster that the legendary hero Scarlet only succeeded in sealing away, and spearheads the operation to defeat the game's Big Bad. (To say nothing of the postgame content.) Thanks to the game mechanics, it's also perfectly permissable to make her a Lightning Bruiser and have her curbstomp enemies way above her own level without having to rely on her army.
There is a young, lovely, cute, spunky, aloof, innocent, friendly, childish Genki Girl in almost every Final Fantasy game: Rydia, Krile, Relm, Yuffie, Selphie, Eiko, Rikku, Penelo, Vanille. And all of them cover the Badass part of the trope. They are capable to decimate anything, be it with bombs, Black Magic, Summon Magic or just oversized weapons that they shouldn't be able to carry.
Selphie is willing to blow up a whole missile base, and that's just one of her moments. Not to mention she possesses the strongest Limit Break in the entire game, called The End, which will wish the enemy into the flower fields in a one-hit KO. Worst of it all? It works on the final boss.
One of Vanille's "battle sayings" is "I'm not all flowers and sunshine!" In a sickeningly cute, sweet, sing-song voice. You could hear the jaws hit the floor when it was learned that cute and cheery she had a summon that was a walking war machine. Not to mention that she's the harbinger of the apocalypse. Badass indeed.
And Gau. The cute, adorable little feral boy who was Raised by Wolves manages to wear out Sabin, the game's leading badass who can suplex a train, calling it a dance. In battle, Gau is a Disc One Nuke and a Disc Two Tank, who is capable scratching like a cat For Massive Damage.
Serah, Lightning's little sister, is the main character of Final Fantasy XIII-2. Damsel in Distress no more. She possesses fighting skills on par with the party members from the original game now, and she's no less cute from it. Her victory pose is catching Empathic Weapon and Team Pet Mog and giving him a hug.
Sora, Roxas, Ven and Xion from Kingdom Hearts. Still, the absolute best example is none other than Mickey Mouse, who they managed to turn into freaking Yoda, of all things.
His Badass quotient has only increased over the games. In Chain of Memories, he's a support character that appears to cast spells. By II, he's playable whenever Sora is defeated, but can't actually finish off bosses (Although his agile combo actually makes him pretty good at wearing them down) . When 358/2 Days made him playable, he was on about the same level as the other playable characters. By Dream Drop Distance he's capable of pulling a ZA WARUDO on every member of the new Organization XIII (including the Big Bads from I and II) in time. The only person capable of resisting is the incarnation of Xehanort with power over time itself. All this from a former steamboat worker.
Aside from Final Fantasy, The World Ends with You gives us Mr. Mew. An adorable little cat plush that could rip your eyes out.
Super Robot Wars gives us several examples. There's Latooni, The Woobie who is also arguably the best pilot in the Original Generation games; Mai Kobayashi, Tykebomb, one-time end-game boss, and adorable in the extreme; Ibis Douglas, the luckless but tenacious flat chested girl; and even the villain of the second Original Generation game Einst Alfimi, ridiculously moe and ridiculously broken once you manage to recruit her.
Quite a few characters from Fire Emblem can turn out this way.
Amelia can take this to an absurd degree if you make her into a General. Basically, she remains an adorable teenage girl in all of the cutscenes, but on the battlefield she's seven feet tall, covered from head to toe in plate mail, and wields weapons that make Cloud's Buster Sword look like a toothpick. Combine this with positively absurd stat-growth and you have what is basically a walking wall of certain death. An adorable, shy wall of certain death. Ross is a Hot-Blooded boy who idolizes his Retired Badass dad but is quite the sweetheart to others, and Ewan is a cheery prankster with a talent for magic. Raise them well and promote the first one into either a Berserker or a Warrior, while making the other a Summoner or a Druid. The three trainees absolutely Moe killing machines - and double if you get any of the boys to A Support level with Amelia.
And there's plenty more in the Tellius canon: Queen Elincia, Mia, Mist, Sanaki, Ilyana, Rolf, Marcia, Nephenee, Astrid... Take your pick!
Most of the female manaketes throughout the series (Tiki, Fa, Myrrh, and Nono, to be specific) definitely qualify.
Fire Emblem Awakening takes this trope to new levels with Lucina. In the battlefield she's arguably the most badass female character in the entire game, only contested by a female Avatar, and easily enters the Top 5 of the entire series (and that's saying a LOT). But during her support conversations and quite a few cutscences, you just want to hug her dearly just out of sheer cuteness!
Nowi, Nah, Cynthia, Noire, both versions of Morgan...Awakening has quite a few characters that qualify for this.
Ricken. Just don't call him adorable.
You can make one in Spore if you're clever enough.
Gnomes in World of Warcraft, especially the females. That three foot tall gnome with bright pink buns tanking a massive boss four times her size is adorable.
Four times? Meet Supremus, the largest boss currently in the game. A gnome can tank that— it's about 10 to 15 times the size of a night elf (a rather tall character).
Female Pandaren are also super-cute, and exactly as capable of asskicking as any orc or elf.
Ninjabread Man — A cute, little cookie that so happens to know self-defense. Too bad the game blows.
Koromaru from Persona 3. His victory pose is to cutely scratch himself! Ken Amada, as a ten-year-old cute little boy, might also count. The alternative female protagonist of the PSP version definitely does.
Ghost Trick has Missile, a yappy little Pomeranian who is adorable even by Pomeranian standards. After he dies for the second time, he gains ghost trick powers. His reach is far longer than Sissel's and he has the ability to swap objects of different sizes, even huge stone statues.
And in an alternate timeline he waited ten years for the events of that night to play out again, so this time he could convince Sissel to help Lynne.
Sissel is also this, considering he's actually a little black cat. At the end, he's a little black kitten. Awwww.
A few characters from Cave Story. King is a Mimiga (a rabbit-man) who takes out Balrog with a single swordstroke. Then there's Quote and Curly who... well, just look at this in-game art◊, depicting them in the act of stormingHell.
Ar tonelico has Cocona Bartel in the second game. She's about ten years old or so, four-foot-nothing, wears her long hair in pigtails with two absurdly large hair ornaments, and is the main character's adopted little sister. She is a very cheery girl who is always willing to help her big brother and often pouts in the cutest way whenever he's late. Turns out that she accompanies her "big brother" on his knight missions, and fights by taking her hair ornaments off and using them as a sort of transforming baton weapon. Despite her size, she keeps up with the adult frontline fighters, including her older brother. And the kicker? She is a Reyvateil, a species that is usually kept in the back lines far away from the physical fighting. Also thanks to her BFS in her Limit Break.
The campers of Psychonauts are all pre-teen psychics in-training. Most notable is Raz, who not only learns several potent psychic techniques but is also a skilled acrobat due to his life as a GypsyCircus Brat.
In the first game, Liara and Tali. Liara is a socially awkward archaeologist that has never been in a relationship before, and can scatter enemy troopers like papers in a hurricane and crush tanks like tin cans. Tali is Naďve Newcomer that, similarly to Liara, has never been in a relationship, but can shut down your shields, make your weapons explode, and poison your nervous system with a few taps on her omni-tool.
Note that, with the serious turn towards the dark that happens in Mass Effect 2, the "adorable" factor for these two gets reduced. In the two years between the games, Shepard's death, Cerberus' attack on the Migrant Fleet, Liara's newfound obsession with the Shadow Broker, and the Collector attacks, the galaxy has become a much rougher place, particularly for these two. Tali becomes adorable (and Adorkable) again in her romance, as does Liara if you have Lair of the Shadow Broker added. By the time Mass Effect 3 rolls around, though, Liara and Tali are just as hard and weary as every other character.
The Retaliation DLC for Mass Effect 3 allows you to play as a volus in multiplayer.
Ratchet & Clank. A cute little fuzzy alien with big round eyes, an incredibly expressive face, and enough weaponry to take down a dozen intergalactic armies..... literally, and his cute little robot friend, a secret agent who can grow into a Godzilla sized living weapon and control time. Saving all of time and space while looking incredibly cute.
As stated, a good number of Pokémon and even their trainers.
But no mention of Mew? The progenitor of all other Pokémon? I mean, it only does EVERYTHING.
All "cute legendaries" (Mew, Celebi, Jirachi, Manaphy, Shaymin, Victini) qualify. Notably Jirachi has a creepy eye, Celebi can Time Travel, and Shaymin transforms into a more badass form.
Which is arguably even cuter than its Land Forme.
The protagonists and their rivals are almost always this, except for a few side game ones who are older.
Iris is one. Drayden's assistant in Black, Gym Leader in White and Champion in the sequels. She also pretends to do a roar at the beginning of battle... and then she sends out a Hydreigon.
Ukulele Pichu from Guardian Signs. Unlike all other Pokémon, it will still do the assist even if it's hit by Beam Spam/whatever-attack of Pokémon engineered to be the most powerful one (Mewtwo) or even the god ITSELF (Arceus).
Sylveon of Gen VI immediately gained this reputation once people learned of its type and what it's capable of doing. That badass Garchomp you're holding? Sylveon will eat it and ask for seconds.
Rebecca Chambers, from the Resident Evil series. Originally just a pixie-esque medic, we later learn that she fought her way through a night of Lovecraftian horrors before Chris Redfield ever saw his first zombie. Also, in her cameo in the "Mercenaries Reunion" mode in Resident Evil 5, she sets people on fire.
Dog from Dragon Age: Origins. While outwardly he's a Big Friendly Dog the size of a small pony, he's actually a Mabari; a special breed of War-dogs created by Tevinter Magisters to be as intelligent as a human. Contingents of Mabari have traditionally served as elite units in the Ferelden army and used for breaking enemy formations and taking down Knights. While travelling with the Warden, Dog will jump headfirst into the fray and tear his enemies to pieces, before coming back covered in blood, wagging his tail and waiting to be scratched behind the ears by his Master. Sten considers him a true warrior, Oghren is convinced he's trying to steal his pants and Morrigan complains that he keeps leaving dead rabbits in her pack, because he thinks she needs toeat more.
And of course, his counterpart in Dragon Age II. Hawke's companions will occasionally come to their home simply to visit the Dog, Varric plays regular games of cards with him and Aveline even asks to borrow him to help train the Kirkwall City Guard, so they can learn how people in Ferelden don't soil themselves when they see a massive Mabari charging at them.
In Dragon Age II there is also Merrill. She's a thin, naive, innocent, sweet-natured, easily distracted, practicing blood mage and Demon Summoner who becomes a Motor Mouth when nervous. She also has only offensive magic and vicious combat buffs, not even the slightest healing spell, and fearsome drive to revive the glory of Arlathan for which she is willing to sacrifice her life. Absolutely Adorkable and she can a-splode you from half a mile away with her mind.
The Pet Dragon from King's Bounty: Armored Princess. Basically, a winged technicolored Stitch, who likes to play with a little snail and dance around his pot tree (check him out). Oh, look, he's summoning fountains of lava to engulf the enemies in searing agony, conjures lightning balls and finishes the surviviors off with a somersault kick. Awww!
Sunny from Metal Gear Solid 4. Seven years old, cute as a button, and able to take down an AI that has effectively taken over the world.
Otacon, too, for that matter. Combine his male-Meganekko-osity, shyness, niceness, and nerdiness with his genius hacker-dom, the fact that he's the creator of freakin' Metal Gear Rex, and his Heroic Sacrifice tendencies, and you get one true Badass Adorable.
Dr. Fetus fom Super Meat Boy. He may be pretty ugly and be disgusting in some ways, like when you really acknowledge that he's a fetus, but that little fetus body is just adorable!
Really, almost the entire cast qualifies. Yes, even Bandage Girl.
Little Nana of Vanguard Bandits who's around twelve, has her hair up in pig-tails and is always followed by her platypus pal Kyu-Kyu, is fully capable of being a terror on the battlefield with her personal ATAC even when under-leveled.
Klonoa, anybody? He's an adorable cat-like creature with big long ears. He could also throw you across the screen.
Jedi Consulars get Nadia Grell for a Padawan. The Spoiled Sweet daughter of a Senator (and only known Force Sensitive member of her species) who looks like a strong breeze could whisk her away, utterly Adorkable...and things explode when she gets too excited because she has the strongest raw talent in Force telekenesis the Order's seen in a generation.
On the Imperial side of The Old Republic we have the Bounty Hunter's first companion Mako. Despite working in a distinctly amoral career she constantly supports light-sided actions and takes the time to comfort a woman terrified out of her mind after you two just shot your way into the building. As for the badass side of the equation, we'll let the girl speak for herself:
"I'm not just the pretty sidekick, buster!"
Hunters also get Blizz. He's a Jawa, ya know those cute robed little guys with glowy yellow eyes? He's small, even by their standards. Calls you "Boss." As excitable and cheery as a sugar-high squirrel. Somehow manages to carry a rocket-launcher under his cloak. Mechanically, he's a tank.
Also on the Imperial side we have Ashara, the Sith Inquisitor's melee DPS. She's calm, quiet, contemplative, gets rather nervous when the possibility of a relationship is approached, and will murder you with two lightsabers if she feels it's necessary.
The twins, March and Salsa. A pair of a adorable 8-year-old girls, one sweet and polite, the other something of a hothead. They wield twin chakrams, have access to powerful moves, and... are those sharp teeth and miniature skulls on those necklaces? On the other hand, their headgear is reminiscent of bunnies.
Beat, an 8-year-old boy who is sort of like a younger brother to Allegretto. He wields a repeating rifle with precision.
If you are going to call Mazzy, the halfling pseudo-paladin from Baldur's Gate II this, you're well advised to do it somewhere where she can't hear you.
Mazzy:I won't seem so cute when I break your legs!
One of the default animals in Tokyo Jungle is a feral Pomeranian dog... who is still able to bring down gazelles with a well-timed Clean Kill.
Practically any character (even yours) in Happy Wars.
In Arcanum, there is a spell to summon a wild animal to help you in combat. The animals get progressively stronger depending on how good your character is with magick. They go from wolves to cougars, to tigers, to gorillas and finally, strongest of them all, ... a fluffy white bunny rabbit. Yes, the Vorpal Bunny is a level 40 creature with extremely high strength, maxed out melee and dodge skills and Master level proficiency in both.
Being a fighting game with a variety of characters, the Soul Series is bound to have some adorable folks kicking ass. Although the biggest one is probably Pyrrha Alexandra, who is able to wield SoulEdge without losing her soul to it.
A number of champions from League of Legends are members of the local "adorable midget" race, the yordles, like Poppy the Iron Ambassador and Veigar the Tiny Master of Evil.
And Fizz. He's the cutest sea critter in the league that strongly resembles to Stitch.
Several fighters from the Tekken series, including (but not limited to) Ling Xiaoyu (all-around friendly Genki Girl who one day dreams of building an amusement park), Panda (pet/bodyguard of Xiaoyu), Lili de Rochefort (Spoiled Sweet with love for street fighting) and Alisa Bosconovitch (cute, rose-haired girl who is actually a robot with chainsaws built into her arms).
Juliet Starling from Lollipop Chainsaw. A cute blonde cheerleader who kills zombies with a pink chainsaw. Enough said.