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.