The Trope Namer is Green Mega Man (The Mega-speaking, mega-hyperactive, mega-side kick from Captain N), from Captain SNES: The Game Masta. Even the Cynical, rude, and foul-mouthed bastard that is Alex Williams, thinks Green Mega is Adorably Badass.
Ruby Gem, the little toddler vampire girl from Monsterful.
Even more Badass when she transforms into a VSV (Vampiric Spartan Viking).
Several of the younger characters in Drowtales are like this due to the way drow age making them look like young children even when in their 20s, but Ariel is probably the best example, since she looks about 8 and has already kicked the asses of several people who've gone after her. Generally speaking even cute little kids in Drowtales can kick loads of ass since they live in a Crapsack World and pretty much have to in order to stay alive.
Most of the cast of Digger is this. Digger herself, Ed, Shadowchild, Murai...
Sluggy Freelance has had a few including Princess-Princess who is really Secret Angel Princess-Princess. Especially when she figures out how stupid that sounds out loud. Secret Cranky Office Temp could also qualify. Aylee in a couple of her forms was adorable and could either swallow you whole or burn you to a crisp. Obviously Oasis, the ultimate cutie when she's not taking out entire armies single handed. Being bat-shit insane can have her going from one to the other in nanoseconds. And then there is Bun Bun; a cute little mini-lop with floppy ears, aww. That is until you look deep into those big dark eyes and see how much you are going to suffer if you don't get out of his face right now, toots.
Sugar Bits. Bleedman is possibly the only person in the world who can make a cookie badass. And this is without mentioning Bo, the ridiculously adorable and tiny sheep... who will do this if you screw with her friends.
The Racconans from Tales of the Questor are an entire nation of tiny Raccoon-like humanoids... ...Nearly all of which can unleash powerful magics in self-defence, have perfected magical engineering to the point they're nearly an industrial power in an age of knights and castles, and most Racconan communities have huge militias. Add to that an attitude of combat pragmatism and an insidious cunning, and you have a nation of 2 foot tall critters that has thus far squashed every invasion thus attempted on it's territory. The Racconans could teach the Ewoks a few lessons.
In the same vein as Earthbound, the kids from Homestuck, even the Ugly Cute Trolls. Yes, those are thirteen-year-old tykes, casually manipulating time, space and the universe itself, fighting hordes that make the Zerg look conservative and blowing up stars.(Special mention goes to Rose and Nepeta.)
Taken up to eleven with Jade's God Tier form, which gave her her pet dog's Reality Warper powers - and dog ears.
Several characters in Kevin & Kell qualify, but the undisputed champion is Coney Dewclaw, a three-year-old diaper-wearing bunny rabbit. She's also half-wolf (on her mother's side), and effortlessly devours slavering carnivores five times her size in a single panel.
The Oswald Chronicles's eponymous Oswald, a mouse with pince-nez glasses, a bow-tie and a vest. Also, enough magical mojo to go toe to toe with the greatest sorcerer alive.
Morty of Suppression is described as a walking sphere of primal, powerful magic energy. He has (in teaming up with Kirk) devastated demons much larger than him and taken out an entire row of houses after turning into a BFG. And he is absolutely adorable.
While the titular character of Charby the Vampirate is stuck looking like an cute if sharp toothed kid, he took out a ship full of pirates on his ninth birthday, and has only gotten cooler since then.
Jack Hawkin from Zokusho Comics is a foot shorter than anyone else on his team and considerably younger. He is obviously extremely pleased by a simple compliment on his chess playing abilities. Just a few pages later he's calling down lightning to fry the enemies he isn't just setting on fire.
Platypus from Vinigortonio may look like an ordinary platypus but can actually hold his own in a fight and even infiltrate the police department without being noticed.
The three main protagonists of Gunnerkrigg Court. Annie has befriended gods, Kat has somehow become a semi-divine figure to an entire society, and Renard is a body-shifting fox-demon who is easily one of the scariest things in the whole series. Annie and Kat are 13/14 years old. Renard is currently in the body of a toy wolf.
Fred of Namesake. He literally exists to be a soldier and is lethal with a pair of daggers, taking down sword fighters and supernatural ghost-things alike, as well as picking up and carrying a grown woman despite being around five feet tall. He is also extremely naive, awkward and sweet, gets both excited and confused about human things like sandwiches, and is completely smitten with the girl who accidentally granted him several human characteristics. Just look at this interview. To quote a reader on that page: "Fred's so fucking cute he can say another card was destroyed in battle and all I wanna do is pinch his stupid cheeks."
Kexas from the sprite comic Kirby's Dream Adventure is a good example. Being a kirby, she's adorable by default, and she's the champion of the arena, being borderline God-Mode Sue thanks to her raw physical strength and access to a permanent Crash ability. Her name even sounds like "kicks-ass".