Cloud Williams. He falls to pieces around his girlfriend and he's a video game nerd, to boot. But he's also a trained swordsman and he can kick your ass, big time.
David and Ye Thuza, Cloud's parents. They're huge Final Fantasy nerds (to the point where they named their kids Cloud and Yuna), they're bronies, and they act like adorable children when they're at a restaurant.
Landon is a nerdy, sweet guy who does everything he can to make his girlfriend happy.
Criminy from Sinfest embodies the trope, to the point that one of the resident Horny Devils has fallen head-over-heels for him.
Sabrina's boyfriend R.C. is Adorkable, and he collects anime figurines.
Kia the Succubus of Krakow Comics calls her boyfriend ( later her husband) her "naughty, gawky Cinderella".
Theo, of The Noordegraaf Files is a programmer with little to no idea on how to get a girlfriend - but he's also a nice, caring guy. It doesn't take much time for one of the comic's females to admit they find him "kinda cute".
Davis, the comic's resident effeminate Gadgeteer Genius might also count as this.
Jade of Agents of the Realm can be adorkable sometimes when she's not in The Mentor mode. On her first conversation with Norah, she apologizes profoundly that she can't help her, because she messed up the pages of the instruction and spends quite some time half-apologizing, half-searching for the missing page.
Jake. Especially when talking to Aranea. Although he prefers to think of himself as an Action Hero type, his kind (and slightly ditzy) personality, relentless enthusiasm and optimism, naivete, and weird and yet somehow unself-aware old-fashioned manner of speaking (which Roxy specifically states as one of his most attractive qualities) only point to this trope.
Dave Strider. Most people seem to forget that he's at heart a 13-year-old kid who likes photography and keeping dead things preserved in jars.
Jade Harley. She's an absolutely scatterbrained and yet absolutely adorable girl raised by a dog on an island with a whole shitton of science.
Juvenile Diversion gives us Chris, the youngest, smartest, and geekiest of the protagonists. Naturally, this is why Evie is attracted to him.
Kiley is very insecure and prone to break down crying.
Lance and Dustin from Weregeek. Check out when Dustin was nervous about his date, and the Dec '10 comic where Alina actually uses the word. But the beards on those guys makes it a little more Gentle Bear than Wide Eyed Smiling Ugly Nerd.
Dani is a bespectacled, socially awkward and fairly adorable in her own right teenage girl who just happens to be magically pregnant with a demigod.
Adam is an oft-cheerful young comic book geek (for lack of a better term), with a tendency to say things the wrong way. He's also in love with his best friend Caitlyn, who's in the same boat as Dani a decent chunk of Adam's awkwardness comes from the fact that this isn't exactly a turn-off for him.
While many characters in Girl Genius have Adorkable aspects, the main three characters, Agatha, Gil, and Tarvek, are often very adorkable. This could be because adorkableness is correlated with science and geekiness, and Girl Genius is based on the adventures of Agatha, a mad scientist herself, who tends to attract other mad scientists (aka Sparks). Theo, another Spark, also has a high adorkability quotient. It could simply be that Sparks have a high potential for adorkableness when they're not Axe-Crazy.
Charlotte of Paranormal Mystery Squad and Vampire Cheerleaders has various shades of this trope. She regularly fumbles with her spells, works old tv show and movie references into them ranging from He-Man to Captain Marvel, has a somewhat subtle case of type one big breasts, big deal, and when Katie discusses her in a way that sounds just a little too much like an innuendo her only reaction is pull her knees up to her chest saying "I'll be curling up into my shell now."
Sunstone gives us Ally; successful self made woman, millionaire, impeccably dressed, sexually confident, BDSM dominant and complete spaz.
The protagonist of Explorers of Souls, Mel, is a sarcastic, awkward, adorable, fluffy little Mon who used to play Pokemon games and read fanfiction. How could you not love her?
Grrl Power Sydney Scoville Jr. is the cute tomboy lead with considerable comic and nerd culture proficiency.
In Godslave, Edith's boss at the restaurant is a Nice Guy who smiles a lot, calls her his "bombae" and is genuinely upset and awkwardly trying to cheer her up when he has to fire her temporarily.
God of High School has the protagonist, who acts like a Manchild at time despite being seventeen. Some of his childish behavior includes pressing his face against glass in an attempt to eavesdrop, blatantly providing his grandfather's location out of sheer naive honesty, and yelling "I dun wanna!" when something displeases him while drawn in chibi format.
Sun Jing, a Tomboy who enjoys playing basketball with her male classmates and being The Gadfly to her best friend, is prone to becoming an awkward and flustered mess around Qiu Tong, a girl from a neighboring school she develops a crush on.
Qiu Tong reveals a number of Adorkable traits, being a kind but somewhat socially awkward girl who has trouble interacting with others. She also is starting to grow flustered around Sun Jing with greater frequency after the latter's Love Confession. And she enjoys splashing in rain puddles.
Realized that, as the winner, he was in the hot seat to select who out of the competition would be eliminated: "Uh"
Sorlie in Schlock Mercenary is a UNS military officer who geeks out over rare technology, and only gets involved because she's drafted to serve as a "cultural liaison". In a subsequent book, her reaction to hearing that the Oafa have a gargantuan space station is "I have cultural liaison experience and I want to go I want to go I want to go".