In Pokémon, there was once a wild Teddiursa that behaved like this to get food from trainers and tourists. He became a nuisance until he evolved into Ursaring, when he couldn't use his charms to get stuff anymore. Except from Team Rocket.
Two regions later in Sinnoh, a Togepi played everyone for saps to get full run of Team Rocket's new base. Including the built-in space rocket.
The very powerful and very evil Demon Lord Hellmaster Fibrizo often takes the form of a young child to deceive people. He fools everyone who sees him, up to and including another Demon Lord. The only one to see through his disguise is Xelloss, who in any case is openly working for him. Sort of. For a while, anyway. In the manga, Fibrizo takes the form of a girl who happens to also be an actual character from Lina's past. When Fibrizo is defeated, the girl is set free, so it might have been some sort of possession.
Lina herself has been known to do this occasionally (prominently early in the first novel), taking advantage of her slight build and, ah, flat figure to appear cute, harmless and slightly ditzy.
Conan Edogawa often does this to throw people off from suspecting he's really seventeen year old Shinichi Kudo. Though he can on occasion take it too far and has a time or two been called out by his kid friends for doing it. The really impressive part is that, when he's nosing around crime scenes, he has to walk a very fine line so that his adorable-little-kidness draws the adults' attention to important clues, without drawing their attention to how frequently this happens (or, worse, that he's doing it deliberately), and for the most part, he pulls it off.
Murumo, the little brother of the main character of Mirumo De Pon! acts like the sweetest kid in front of most people, but his dark side is usually revealed to the audience and his older brother. One of his image songs is about this trope.
In Baccano!'s successor series Durarara!!, Aoba is one. He's so good at pulling it off that he's managed to frame his brother for many crimes as well as getting away with many of them. Add the fact that he's described with a baby face despite being a high school student. Of course, he lets it slip every now and then...and when he does...
Rita from the Final OVA of Jungle wa Itsumo Hare nochi Guu, who appears to be the nicest person in the whole class, until it turns out she does it selfishly to get praise and make herself happy (In the end, Hare's presence and comforting turn her into a genuinely nice person.) Guu herself does this on occasion, most notably during her introduction.
Pride of Fullmetal Alchemistaka Selim Bradley pretends to be a sweet and kind young boy. In reality, he is a cruel little monster who has a habit of eating his allies when they are no longer of use to him.
Miharu from Nabarino Ou fits this trope to a T. He blushes wildly in order to get his way in what seems like a hundred different situations, from forcing a basketball player on the opposing team to let him make a basket to getting a shopkeeper to give him free clothes.
Stella from Arakawa Under the Bridge appears to be a sugary sweet orphan girl who just wants to give people a big hug when Kou first meets her. She quickly reveals her true nature as a Cute Bruiser with a mean streak who can and will beat him up to hold dominance over him.
Medusa of Soul Eater attempts this once or twice after she takes over the body of a young girl. Doesn't really work, actually.
Medusa: Why do I have to wear this, Mister? It gives my hands ouchies!
In the manga she convinces Spirit to unchain her by appearing cute and so reminding him of his own, not-possessed daughter. Typical Medusa, she pulls off a similar trick in reverse - remind the daughter of her father - on Maka in the Baba Yaga arc. Forget the Clowns, pulling such simple tricks (justifiably, given who and how) like that is why she, not Asura, is the proper Big Bad.
Broken Blade's Niko borderlines on a codifier of the trope. She's an Ax-CrazyBlood Knight, older than she looks, and knows exactly what she's doing. The guy caught up in the cuteness? Still reacting that way despite coming across her with her gun pointed at someone's head and her knife pointed at his crotch.
The master of this trope is Ciel Phantomhive, at least in the manga. He's cold and calculating (unless you're Lizzie) to a vicious degree...and he will remind you every chance he gets if you work with him. Even then, however, when he acts his age, you may still fall into the trap. Ask the resident Funny Foreigner. However, the Phantomhive Manor Murder arc averted this as hard as it could: everyone present aside from Arthur Conan Doyle was well aware that Ciel was mentally capable of anything from being adorable and sweet to cold blooded murder. And then played it straight at the same time, by tricking Arthur- the only person there who didn't know of Ciel's reputation beforehand- into thinking of Ciel as a child with too much responsibilities who mostly pretends to be stronger and colder then he is.
A more innocent version of this trope is Ciel's cousin/fiancee Lizzie who just wants to be a proper girly-girl, not a tough sword-fighting Little Miss Bad Ass.
Though a little older than most examples of this trope, Yokosuka Jou from Rainbow Nisha Rokubou No Shichinin learns to use his innocuous beauty to manipulate the perverted doctor working at the reformatory institute he is held. In the ensuing conversation, he plays up his cuteness by switching pronouns, using the more soft-spoken 'boku' rather than the rough 'ore' he ordinarily employs.
Molly Hayes from Runaways is a slightly older (eleven at the opening of the story) variation.
In the All Ages Power Pack comics, Franklin Richards uses this on a ticket collector when he and Mass Master run away, complete with lisp and puppy dog eyes.
In the first arc of Touhou Ibunshu, Rumia combines this with a Wounded Gazelle Gambit to manipulate Remiu into removing her ribbon. Later, Reimu falls for this again when Remilia pretends to a scared child helping her escape, only to eventually turn on her.
Orphan has Esther Coleman, who can charm any adult she wants with her carefully calculated veneer of wistful cuteness. It's so deliberate she even wears her hair in curls and only dresses in old fashioned classic little girl clothing.
In Kick-Ass, Mindy pulls this trick on D'Amico's goons by showing up at his place in school uniform and pig-tails, claiming to have lost her mommy and daddy. It doesn't work out well for the goons.
In Interview with the Vampire, Claudia uses this kind of behavior to lure and play with her prey. One particular scene shows her sitting on a bench crying and letting the woman who comes to help her hug for longer than necessary before biting her.
Harley tries to use this tactic on Tony Stark in Iron Man 3 so he could be his Tagalong Kid. However, Tony realizes what he's doing and instead redirects the impact of the ruse back as a trollish remark.
Tony: Wait, you're guilt tripping me, aren't you? Harley:I'm cold. Tony: I can tell. You know how I can tell? Cause we're connected. [Drives away] Harley: It was worth a shot.
Twyla: I'm afwaid of the monster in the cellar, Thusan. It's going to eat me up.
Susan: What have I told you about trying to sound ingratiatingly cute, Twyla?"
Twyla: You said I mustn't. You said that exaggerated lisping is a hanging offense and I only do it to get attention.
Twinkle from House of Many Ways by Diana Wynne Jones, who falls into the Really 700 Years Old box. Well, 'Really About Thirty'. He has a good reason for it: he's deliberately drawing attention away from the real child, his son, so that any potential kidnappers will go after him instead. It works, too.
When April from "Dustbin Baby" enters into her fourth foster home, she realizes that one of the older girls will like her better if she acts this way. Because April is a little lost and needs a friend and caregiver, she obliges.
Aphrael, the Child-Goddess of David Eddings' Elenium and Tamuli: As her name suggests, she constantly retains the form of a child, and just as constantly uses this to manipulate others into giving her what she wants. To her credit, she feels genuine love and affection for those around her and goes to great lengths for their protection.
Baby Dwopple in the Redwall book Marlfox steals food and shoots adults with a miniature sling, then clings to his adoptive mother weeping and exaggerating his Baby Talk beyond even usual Dibbun levels until she yells at the others for trying to tell him off.
Markie in Little Myth Marker does adorable little kid things like mispronouncing words, and bluntly spitting out offensive statements. She turns out to be an character assassin sent to ruin Skeeve's reputation, and a full grown woman to boot; natives of her dimension just happen to look like seven-year-old Klahds their entire lives.
Willie Connolly in the J.R. Lowell novel Daughter Of Darkness carefully maintains a facade as a darling, adorable and very happy Child Prodigy. She really is twelve, but that's about it.
In Mark Clifton's novella "Star Bright", five-year-old Star Holmes has an IQ somewhere in the quadruple digits, but is legally required to go to kindergarten, so she pulls an adorable-dimwit act. The class leader (a "stupid" — that is, someone of normal intelligence) takes charge of her and tells everyone they have to like her.
As the page image shows, Calvin does this repeatedly with varying success.
Babette, a 300-year old vampire and member of the Dark Brotherhood (assassin's guild) in The Elder Scrolls V: Skyrim. She became a vampire at age 8, so that's how she still appears, and uses this appearance to her advantage.
Remember that little girl that got captured at the beginning of Ratchet & Clank: Size Matters? Turns out she's actually a puppet created by tiny monsters to fool the protagonists into rescuing "her" so that the Big Bad can clone one of them.
From Higurashi: When They Cry, Rika Furude is universally adored by everyone in the town, especially her friends. However, she's also fully aware of the town's "Groundhog Day" Loop, and remembers all of her past lives, meaning she's arguably one of the oldest and wisest people in Hinamizawa, despite being stuck in the body of a prepubescent girl. She is extremely unsettling whenever she drops her cheerful and innocent facade, to the point that the sharp contrast can easily be misattributed to Demonic Possession in the early chapters (before the audience understands what's really happening in Hinamizawa). Her reason for adopting the Cheerful Child persona is less about manipulating people and more about not wanting to alarm anyone unless the situation is serious.
Annie of Catena uses this (and a flail) to get into a D&D game.
Though adult, Kalki from Drowtales really pushes the borders of cutesy behaviour. She's probably trying to avoid being associated with the mass slaughter she took part in some years back.
Autumn of Precocious uses a schoolgirl uniform to try to invoke this in others. Dionne is also said to do this when enrolled a beauty pageant; off the clock, she prefers her throne of bones.
Tweety Bird of Looney Tunes fame. "Aw, da poor puddy tat. He faw down an' go Boom!" This, after carefully arranging poor Sylvester's defeat.
Charley, a frequently abandoned dog who appeared in a few Chuck Jones cartoons also employed this trope. "Big soulful eyes routine. Gets 'em every time." When people walk on past and ignore him, he remarks, "Well, nearly every time."
In the Chuck Jones cartoon "Baby Buggy Bunny", diminutive bank robber Baby Face Finster, aka Ant Hill Harry, impersonates an adorable baby to evade the police, and later infiltrates Bugs Bunny's rabbit hole when Bugs accidentally gets his hands on his stolen money. Bugs falls for it initially. Once he realizes he's been had, it's bad news for Finster.
The one-shot characters called the Cuddlemuffins from My Gym Partner's a Monkey. They pretend to be very cute for Adam so that they can take his money to buy food pellets, which they do CONSTANTLY. Jake, Slips, and Windsor eventually help Adam when he sells his hair to pay the Cuddlemuffins off, but when they show up to act cute towards their next 3 victims, Adam stops it once and for all by shaving off the Cuddlemuffins' coats, as well as his friends'.
In Fillmore!, Cornelius Fillmore and Ingrid Third are on their way to a store to get evidence. By the time they get there, the store's closed. In order to charm the store owner into letting them in Ingrid, normally a Perky Goth, announces, "I'm going to have to use my cute face. This won't be pretty." Later, Fillmore comments, "You sure took one for the team, Ingrid."
June of KaBlam!!. If you were to look at the "cute" act she puts on every once and a while, with no prior knowledge of her character, you wouldn't guess that she's one of the most (if not the most) hot-headed characters on the show.
Appeared on an episode of The Critic when Jay's boss tried to improve his image. Jay suggests having his son appear on the show with him - but rather than use Jay's actual son, his boss brings in a child actor whose cuteness comes complete with an "adowable" speech impediment. When Jay declares the kid "wepuwsive" the boy's voice goes down an octave, the impediment disappears, and he informs (in a Brooklyn accent) Jay that the speech impediment is trademarked.
Dot Warner of Animaniacs exploits her cuteness for all it's worth.
Claire from Titan Maximum is a twenty-one year old, who looks eight, but she also talks and acts eight, complete with an obsession for cuteness, and using words such as "sowwy". She's also an expert assassin.
Wilykat and Wilykit in ThunderCats (2011) are Catfolkkittens, depicted as a pair of Artful Dodgers who survived the slums of Thundera by playing up their cuteness when they weren't simply outsmarting and running circles around their targets. This is especially obvious when they first ask if they can tag along with Lion-O's group after Thundera is sacked, complete with Faux Paw and kittenish mewling.
Gideon Gleeful of Gravity Falls uses this whenever he can to get out of trouble.
The The Powerpuff Girls episode "Sweet N Sour" had oneshot villains which were three adorable baby animals who held up banks and jewelry stores. But since they were SO CUTE the clerks in the store just give them everything, and if the Powerpuff Girls so much as come near them, THEY will be labeled as the bad guys. In truth, the three cute animals are rude, manipulative, greedy, and threaten the Girls that they will invoke this trope if they try and put them in jail. And they DO.