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 his being Sarcasm-Blind).
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.
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.
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.
Diana Allers, a reporter Shepard may choose to bring on board the Normandy in ME3. If Shepard plays nice and doesn't kick her off the ship, he or she gets to make out with Diana at one point.
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.
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.
Super Mario Bros.: Luigi becomes more Adorkable every game. He's clumsier than his better-renowned brother 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.
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.
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 Urn by dropping it in paint. There's also her co-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.
Miles Edgeworth often behaves as adorable dork, especially when it comes to trying to loosen up and when he interacts with his not-so-secret love of the Steel Samurai.
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, Desiree.
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 comments on professing his love to Regina Berry in his inner monologue, because of how cute she is. 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.
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 woman with a poor understanding of emotions, something even her stoic brother, Miles, understands.
10 of Spades, a Friendly Sniper. He's the shortest character in the game, one of the friendliest, has a stutter, and wears thick Nerd Glasses. Unfortunately, he sometimes disappears from the game after a quest is completed.
Travis Touchdown from No More Heroes, when he's outside of missions, he's like a big grown up nerd who has to keep on doing his best to live a normal life despite being a total badass assassin.
Tales of Vesperia: 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.
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 which makes this a subversion and a half of the Bad Ass trope.
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.
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!
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)."
Kid Icarus: Uprising: Pit, despite being a competent fighter, has an upbeat and somewhat childish personality. He likes to look tough, but he's such a cute kid that you usually can't help but chuckle at his attempts. It's no wonder the other characters make fun of him so much.