Gaige in Borderlands 2 has "Excessive Adorability" on her "Wanted!" Poster. She's a tiny, slightly built nerd with Girlish Pigtails who speaks in L33t L1ng0, references My Little Pony: Friendship Is Magic, and built her very own robot to deal with bullies (and may have overengineered it a little). One of her ECHO casts has her berate her father for bringing in cocoa while she's trying to come across as badass, then drink it anyway. This being Borderlands 2, she's still a maniac who gets a Power High from building Anarchy stacks, but she's still pretty cute.
If you are a main character in a Kingdom Hearts game, you are probably some shade of Adorkable.
Sora, especially in the first game. In the later games, he Takes A Level In Emo, but he still has a distinct boyish enthusiasm and optimism.
Ventus is possibly even more adorkable than Sora given his nature, which is only highlighted when he interacts with Zack and Hercules.
Riku gets a shade of this in Dream Drop Distance when Shiki starts flirting with him and he's utterly flabbergasted. Lampshaded when she asks if he "gets out much".
Roxas and Xion, when they're not having their bouts of melancholy, take after Sora and Ven (obviously.)
Neku Sakuraba, a Defrosting Ice Queen with a penchant for social awkwardness and massive fanboyism when it comes to his favorite artist, CAT. In Another Day, this gets expanded on even more, with him being a massive fanboy of Tin Pin who collects his favorite Tin Pin Weekly issues in a acid-proof scrapbook who also purposely styles his Shonen Hair after manga, of all things. This even gets lampshaded by the other characters, who call him a massive geek after learning this.
Daisukenojo "Beat" Bito, a Idiot Hero skater with a penchant for comical overreactions, Malaproper word play, and being a genuine softie underneath his tough guy act, especially when it comes to his friends and sister, Rhyme.
There's also Priam, the descendant of the Hero of the Blue Flames. Of course, he's a massive badass with a great skill set, but when he starts developing feelings for a Female Robin, he starts blushing like mad and even yells "HUZZAH!" when she returns his feelings.
Takumi and Leo are both strong contenders. While they each try to project an aura of maturity, they are actually quite dorky. Takumi turns into a stuttering mess during his supports with Camilla, clearly shows his fear of the Faceless over his vehement denials, and is generally easy to fluster with compliments. Despite his perfectionist tendencies, Leo has the odd habit of accidentally wearing his clothes inside out and completely freaks out when it is brought up. In his attempts to have his older siblings praise him, he also often comes off as a starving puppy.
Our protagonist Corrin. While he/she has a great amount of skill and charisma as a warrior, s/he's so socially inept but so well-meaning it comes across as endearing. And then you have him/her S-support someone and watch him/her either a) fluster his/her way through a confession or b) get extraordinary flustered by their confession.
Katsuya Suou from Persona 2: Eternal Punishment is a cop who wonders if the penal code applies to demons, and he will even interrogate them as a contact option! Her also has a HUGE crush on Maya Amano, and because he's got a crippling case of Cannot Spit It Out, he calls her Ms. Amano, even towards the end of the game.
Unexpectedly, Akihiko Sanada - who initially comes across as a cool, self-assured upperclassman and is the most sought-after boy at Gekkoukan High School - turns out to be completely adorkable when it comes to actually interacting with girls outside of SEES. The PSP re-release turns it Up to Eleven by making him a possible love interest for the female protagonist.
Shinjiro Aragaki, of all people, also turns out to have a bit of this going on thanks to a hidden love of animals and cooking shows, though he's more a gruffly Sugar-and-Ice Personality than outright dorky. Again, it's played up in the PSP version thanks to his Social Link in the female main character's route.
Theodore, Igor's male assistant in the PSP version (if you play as the female protagonist) is smooth and calm in the Velvet Room, but if you take him out to explore the human world, he quickly shows himself to be this, with his Fish out of Water tendencies and his childlike wonder and uncertainty about the ways of the human world (to say nothing of him being Sarcasm-Blind).
This is the common reaction to Naoto Shirogane despite (or because of) the fact that she is a girl. Normally speaks in a very mature and intellectual fashion, but can start gushing over anything that relates to her interests in detective novels, solving mysteries, action figures and tokusatsu shows; her own Dungeon in the TV World is noted as looking like something out of a sentai or tokusatsu series, her Shadow appears as a sentai-ish cyborg, and even her Personas have that sort of motif. She also gets very easily flustered in social situations, and really gets shy if the player takes her romance path.
Though she normally comes off as a straight-up martial arts loving Big Eatertomboy, Chie Satonaka is pretty adorkable as well as you pursue her Social Link and discover her more feminine traits. She breaks down and starts awkwardly crying in the middle of Junes after Yosuke and the protagonist's second expedition to the TV World, she freaks out when Nanako chirps that there's a grasshopper on Chie's back, and she gets very shy and prone to blabbering during her romance scenes.
As a recovering shut-in, Futaba is very socially awkward and a bit of a Cloudcuckoolander to the point where it became endearing. She is also a huge fan of video games, and makes a bunch of references to them. She gets especially adorable should the player romance her, as once Joker confesses his love to her, she gets incredibly flustered around him, to the point that she completely shuts down for a good eight to nine text boxes.
Haru's introduction as a "rival thief" to the Phantom Thieves is full of it. She actually gets stage fright during her first encounter with them because she hadn't yet thought of a code name for herself and couldn't remember the script she'd prepared with Morgana beforehand.
Like Naoto, Makoto has a pretty serious personality, but she shows shades of this as well. During the Madarame arc (as well as the start of the Kaneshiro arc), she started following Joker around with a manga magazine that she obviously isn't reading. She is also shown to be scared of some "spooky" things as when the Phantom Thieves broke into the Sakura house, this happens. Even in battle, one of her three possible quotes at the end of her All-Out-Attack is her shouting "FIST OF JUSTICE!" in a hilariously hammy manner.
Ryuji tends to get overexcited when talking about upcoming plans for the Phantom Thieves. Ann plays the Straight Man during these moments and shuts him up before he starts yelling about being wanted criminals in public.
Zack Fair in the Compilation, especially the prequels Crisis Core and Before Crisis. Zack is one of the strongest characters in the series, but he STILL manages to have oh so many adorably silly moments. Even pre-Nibelheim (i.e., sane) Sephiroth apparently isn't immune to Zack's adorkable qualities, as seen here.
Cloud and Tifa can both be rather adorkable at times, when they aren't moping about. Especially when moments of sexual tension hit and their shyness and discomfort comes out full blast.
Big Boss (mostly in his younger appearances). He irrationally loves boxes, is scared by horror movies, and believes in Santa because he brought him presents. There's also a scene in Snake Eater where he geeks out over a highly-modified M1911 pistol... ignoring the half-naked woman that brought him the gun in the first place.
Otacon, especially in Metal Gear Solid 4. His backstory and the events of the game make him a huge Woobie, and he becomes easily flustered and has a soft manner of speaking. He has crushes on both Sniper Wolf in the first game and Naomi in the fourth who both end up dying in front of him as he cries pathetically.
Ocelot could almost be considered this in Metal Gear Solid 3: Snake Eater, where he appears as a young GRU Major who tries incredibly hard to be cool, from adopting his signature revolver at a young Big Boss' suggestion to doing incredibly complex and almost silly Gun Twirling.
Shad from The Legend of Zelda: Twilight Princess — a few fans have speculated that he may be some sort of Hyrulean Expy of Otacon. He's also supposedly very similar to Nintendo of America translator Bill Trinen; goodness only knows what that says about Bill.
Link at the beginning of Skyward Sword, notably when he is with Zelda, who seems to have this opinion of him when he holds up her sailcloth. By the end, he has taken several hundred thousand levels in badass.
Breath of the Wild has not only Link, but Princess Zelda herself. Link hums while cooking and cheers when his meal is finished, sometimes has the option to make pretty corny puns, and, if he isn't wearing a shirt, will take time to admire his own physique in a very humorous fashion. Princess Zelda is a Badass Bookworm who, upon seeing a frog, catches up to it on her knees and presents it to Link with a "Ta-Dah!" before excitedly trying to convince Link to eat it to study its effects.
Flower from Magium is a justified example. After fusing with Illuna twenty years ago, she has physically and mentally stopped aging, thus never maturing past ten despite being technically almost in her thirties.
Liara T'Soni, who is able to be romanced by both sexes. A good portion of her romance in the first game has her being easily flustered by Shepard's romances and accidentally, and quite humorously, putting her foot in her mouth. Both attributes were found adorable. And, a lot like Tali, she's a massive woobie.
Legion, if you talk to him and ask why he's wearing your old armor. He reacts with what seems to be the geth version of a blush and then says: "No data available."
Samantha Traynor, the chess-loving comm specialist in the third Mass Effect game, fits this definition to a T. Sadly, for those playing the male Shepard, she's lesbian, but if you play the female version, she does a lot more than just play chess with Shepard.
Maya Brooks in the Mass Effect 3 "Citadel" DLC, maybe more so than any other character in the franchise. At least she appears to be.
The humanoid version of EDI in ME3, especially in her awkward attempts at humor, her nerdy responses to questions like "What are you thinking?" and, definitely, her adorkable attempts at AI/human romance with Joker.
Super Mario Bros.: Luigi becomes more Adorkable every game. He's clumsier than his better-renowned brother, sometimes speaks with a stutter, and often made a Butt-Monkey, but he does get his time to shine both with the rest of the cast and among the fanbase.
Noel Vermillion. She writes poetry, but gets embarrassed reading it to others. She loves pandas. She is constantly apologising to people (in a sweet way, not an annoying way). She's one of the cutest girls in video games, and the most awkward.
Being one part Dating Sim, no game is complete without at least one single character who falls into this category. Among both males and females and across the series, they include Hot Librarian Mary, shy Woobie Cliff, Meganekun Rick, Louis, and Elliot, Mary Expy Sabrina, Shea, Luke (both of which aren't nerdy but are definitely both hilariously and cutely awkward), and Shrinking Violet Candace.
Story of Seasons (2014) introduces Nadi - the Tsundere archetype who's ridiculously sweet and goofy at times, and Lillie, the cheerful and outgoing weather girl who stammers and blushes extremely easily when matters involving love come up.
Ellis. He's a fairly outgoing Keet, but he gets so adorably tongue-tied talking to Zoey.
Louis, with his eternal optimism in the face of zombie hordes, hopeless odds, soul crushing despair and Francis, would seem to qualify.
Lego City Undercover has Frank Honey, the hilariously inept police officer who has boundless optimism and a almost puppy-like excitement for his job despite screwing up pretty much every assignment he's given.
Apollo Justice. His fear of everything and style of lawyering makes him so stupidly cute one begins to wonder how he became a lawyer in the first place. Also, he fanboys over Phoenix until finding out he forged evidence, and his excitement over talking to Vera could be comparable to a high school student on a first date.
Adrian Andrews takes Cute Clumsy Girl to a whole new level by breaking the Kurain Sacred Urn by dropping it in paint. There's also her dependency, which makes her follow the advice of someone else and imitate their personality (as seen with her mentor, Celeste Inpax). Plus, the way she tries to act all tough-as-nails like her mentor makes her more of an example of Sugar-and-Ice Personality rather than your typical Stoic.
Ron DeLite. This guy loses his cool whenever his wife flirts with him, and has a hard time talking without trailing off. He may act like a Gentleman Thief, but he's really this deep down, especially his reaction on getting a letter from his wife, Desirée.
Phoenix Wright himself qualifies as well, to some extent. Especially when he's younger and with a cold. One such example is when he tries talking to Iris. He can barely keep his cool (because she's the twin sister of his former ex-girlfriend) Actually, she impersonated Dahlia and was really the true "Dollie" Phoenix adored. He also denies being a fan of the Steel Samurai, despite having numerous merchandise, much like Edgeworth. Let's face it, this man is just as adorkable, if not more so than Edgeworth due to his regular display of awkwardness.
Franziska von Karma isn't immune, either, once she starts to defrost. Though, her moments are much more subtle than the others. At one point in Case 3-5, she asks Phoenix (in a completely sincere tone, based on his inner commentary when he answers her) if there used to be a lively port town along a river... which is at the bottom of a deep canyon in the mountains. Phoenix notes in the same case that "she's so openly hostile, it's almost cute", which implies that at this point, she's actively trying to be as tsun tsun as possible. She's strongly implied to have a severe Inferiority Superiority Complex thanks to her father and brother, and once you see behind the mask to that insecure side, she's a slightly awkward young girl with a poor understanding of emotions, something even her stoic brother, Miles, understands.
Yuri Lowell, while not a shining example of this due to the serious nature of the story and his role in it most of the time, has his moments in several skits and scenes, especially when interacting with fellow party members Karol and Estelle.
Karol who gets excited about guilds and his heroes and has a Precocious Crush on Nan.
Estelle, geeking out over guilds, books and ancient history.
Banjo-Kazooie: Bottles the Short-Sighted Mole, with his big glasses and vast amounts of knowledge.
Alistair. From the way he quips at Morrigan, to his stories about teasing the cloistered monks who raised him. He's also a Templar trained to murder mages who turn into abominations.
Leliana is incredibly adorkable, especially in her romance sub-plot. She's extraordinarily girly and goofy for someone who's trained in the arts of theft, seduction and murder. She also can acquire a nug and name it "Schmooples".
Zevran displays dorky attractiveness if you venture into his romance sub plot. Normally a dashing Lothario, cold to emotions as his assassin life requires him to be, actual love is something he's not used to dealing with and it shows.
Dragon Age: Inquisition has, believe it or not, Cassandra. Once the player grows closer to her, either as friends or a Love Interest, she lets her tough exterior down and reveals an idealistic romantic underneath. This becomes especially apparent when it's revealed that she's a huge fan of Varric's books, and particularly his smutty romance serials, which he considers to be his worst work.
Cullen, the commander of the Inquisition's military, is as adorkable in personal matters as he is confident on the battlefield. This is only pronounced if he is romanced but if he is, the guy has this in spades. Amusingly, the Inquisitor who romances him has almost the same level of adorkability - a rare thing for a BioWare protagonist.
The Jaws of Hakkon DLC adds Professor Bram Kenric, a visiting staff member from the University of Orlais. He makes terrible jokes, gets so absorbed in his reading that he has to be stopped from walking off ledges while his nose is stuck in a book, and gushes excitedly about history. He's also very cute with a lovely Scottish accent, and according to Scout Harding (with whom he has some slight Ship Tease), he makes a delightful noise when startled.
Guybrush Threepwood from the Monkey Island PC game series is quintessentially adorkable. His first line ever includes an overly exuberant "I wanna be a pirate!" - immediately exposing his adorkable lack of gruff and tough pirate attitude. In his first meeting with the beautiful pirate governor Elaine, he loses all power to speak coherently, uttering words like "blggw" and "dmnkly" (as the game was initially released in 1990, the jokes were in text).
Hikami Itaru from Tokimeki Memorial Girl's Side 2, an intelligent, hard-working, glasses-wearing stickler for the rules who is quite a bit awkward when it comes to girls. If there was ever any doubt, he earns this role in an early CG when the protagonist comes across him wearing a very dorky looking helmet. When she asks, he simply says that it's part of the school rules to wear them and seems confused by the very question.
If you're patient, lucky and adventurous in Tales of Graces, you can catch Hubert becoming this, usually either because of Pascal... or the Sunscreen Rangers:
Hubert: Tonight we feast on dead seafood! Pow Pow!
The title character, in both original and Legend series incarnations. The original Spyro was headstrong and arrogant; despite being the youngest and littlest dragon in the Dragon Realms, which made him a lovable Kid Hero. The Legend series Spyro became even more adorkable from being voiced by Elijah Wood. He was a sweet, intelligent dragon who was always willing to help anyone. And this is despite learning about where he truly came from and who he truly is — The Chosen One. He is suddenly told that he is a rare purple dragon and it is his destiny to save the entire world! On such short notice as well, considering he just learned he was one of the only dragons left and was actually adopted by dragonflies!
Bianca the bunny, who starts out as the Big Bad's #2 lackey. Watching her try to act threatening in spite of her obviously meek, clumsy nature is more cute and funny than anything else. Naturally, this gets her a failing grade in Evil, but makes it that much easier for her to pull a HeelFace Turn when she realizes just how bad her boss actually is.
Salazar: I've sent my right hand to dispose of you.
Leon: Your right hand comes off?
Resident Evil 6 gives us Sherry Birkin who, despite being a rather badass government agent in the same agency as Leon above, still manages to act like an adorkable high school nerd (Maybe it's hiring policy or something). It really shows when she's put with the sarcastic and snide Foil that is Jake Muller, such as when escaping an avalanche on snowmobiles:
Jake: God must really hate us today!
Sherry: Just keep going! We'll make it! Anyway, uh, I don't hate you!
Cousin, who has a good heart and isn't all that skilled at communicating clearly, comes off as this during most of the romances, especially the most awkward bits - stumbling, misunderstanding things, failing to get concepts out clearly, and especially failing to understand what's going on in many situations.
Enthusiastic, chipper, skeptical and somewhat overzealous would-be gumshoe Jane, especially when blundering through inept conversations about weirdness she refuses to accept even exists;
Meowkie, who has a near-perpetual awkward grimace and visible sweat, but is also adorable and extremely enthusiastic about her hall monitor duties (and tuna);
Anti-Bravoman, whose overly dramatic and shadowy attitude hides someone who really, really loves to write terrible poetry;
Military history nerd, bundle of nerves and bully target #1 Blue Max, whose pilot style does not prevent him from being forced to do Taira's homework. For bonus points, his grasp of military lingo includes phrases like "noon hundred hours (that's noon o'clock to you civilians)."
Kormac, your Templar companion in Diablo III is usually a gung-ho warrior who is all about justice and protecting the innocent. But whenever he's around Eirena, the Enchantress of the group, he instantly becomes a shy, tongue-tied, adorable mess who Cannot Spit It Out.
Five Nights at Freddy's 2: The Phone Guy ends up lapsing into this trope when he's talking about how much he loves the animatronics.
Graham, the protagonist of King's Quest (2015), was quite conventionally attractive as a young lad, if a little on the scrawny side, and he had this rather amusing habit of excitedly bouncing around and waving his arms while speculating the awesome properties of some cool things he faces on his adventures, such as that huge impressive-looking scythe in AmayaBlackstone's forge that turns out to be just an overly ornate hedgetrimmer which gets discarded after one use and that strange potion being brewed in the Hobblepot's potion shop which turns out to be tooth-whitening agent... that just turns everything purple unless Graham can get them the right ingredients.
A few characters from the Animal Crossing series may count as this: The biggest is Isabelle, your assistant in New Leaf. Always eager to help you out in Mayoral duties, but can be a bit scatterbrained. Blathers the owl is often seen sleeping, but will talk your ear off if you donate something to the museum. He's also terrified of insects. Quite a few of the villagers may also count as some of them, like the Cranky, Snooty or Smug villagers, who try to put on an air of aloofness or crabbiness, but can be real softies once befriended.
The best representation would be Alphys, Asgore's head scientist. She's incredibly awkward and shy, and is very uncomfortable speaking about anything. She's also extremely friendly once she comes out of her shell.
Papyrus, VERY LOUDSmall Name, Big Ego Royal Guard hopeful. Because, despite those, he's genuinely nice, friendly, and naive. He's the only character who is incapable of killing you (not from lack of strength, but he's too nice). He also sleeps in a racecar bed, owns a bunch of action figures, believes in Santa, loves cooking spaghetti, and if you befriend him he will do everything he can to get you and Undyne to be friends.
King Asgore Dreemurr, who may look scary and intimidating at first, but is, in Papyrus' words, a "big fuzzy pushover". He loves having tea, gardening flowers, and is a notorious Giver of Lame Names.
Undyne is mostly badass, but she does have shades of adorkableness, as she genuinely believes anime is real human history.
Piper Wright, Intrepid Reporter to the Commonwealth Wastelands in Fallout 4, puts on the air of a cocky, devil-may-care journalist who'll leave no stone unturned in her quest for the truth. However, she quickly turns into a flustered, stuttering, babbling wreck whenever the Player Character successfully flirts with her. Certain dialogue options also reveal her to be a bit of a comic book geek.
Alex is a Dragonmaster fanboy who gets to live his dreams and become an awesome hero. Despite this he is humble to the point of bashfulness and lets his girlfriend boss him around. Though that's probably wise since she is a goddess incarnate.
Hiro, the protagonist of Lunar: Eternal Blue, likewise is a fan of Dragonmaster Alex. At one point, he talks a friend into playing lookout for him so he can get on the helm of a certain Cool Boat and pretend he's Dragonmaster Alex without anyone making fun of him. Of course, this is actually just pretext — Hiro's actually after a one-on-one chat with his love interest. But it wouldn't have worked if he didn't like to pretend he's Dragonmaster Alex sometimes.
White Knight Leo starts out as a stern and capable commander (though frequently Played for Laughs). As the story progresses, he softens up and shows a really considerate and cute side — he has a weird fixation on justice and being a super-hero. When he is forced to choose between the letter of the law or the spirit of the law during a major turning-point of the story, he puts on a funny mask and pretends to be a vigilante named "Mystere" instead. His reactions as everyone, one by one, see through his terrible disguise are ridiculous and cute.
Most of the characters of the MySims series qualify, but it especially holds true for any Sim who has Geeky as a primary or secondary Interest.
To put it into perspective: two of the most popular characters are Buddy and Goth Boy. Buddy's primary Interest is Geeky (and has plenty of traits that drive it home), while Goth Boy has it as his secondary (and could probably be seen in his melodramatic nature and love of poetry).
Reinhardt is a 61-year-old man who loves listening to classics like the Hoff, reminiscing on his hair when he was younger, and will ask D.Va, a 19-year-old professional gamer from South Korea of all people for an autograph. Mei is a scientist who is never seen without her adorable smile, optimistic outlook, and her cute sidekick robot, Snowball.
Chiaki Nanami from Super Danganronpa 2 is a Genius DitzGamer Chick who is so invested in her gaming, she forgets to do things like eat, sleep, or even breathe, which results in her often falling asleep in the middle of conversations. She also pauses between sentences and will sometimes end a statement with I think. Her lack of social skills is so bad that shes even hesitant to pet animals, as she has no idea how theyll react and is freaked out by how warm they are.
Evan from MapleStory is a bright and cheerful Adorably Precocious Child who finds himself shoved into the role of the leader of five of the most powerful Living Legends in Maple World. Even as a powerhouse himself, he's easily embarrassed, gets flustered when praised, and stumbles over himself in conversation.
Evan:[After being declared the leader by the other Legends] M-me?! Uh... well, I... don't know if I'm qualified, but I'll try... Erm, I mean...