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troperville

Criminy from Sinfest pretty much embodies the trope, to the point that one of the resident Horny Devils has fallen head-over-heels for him.
Hanna from Hanna Is Not a Boy's Name. He's a 5 ft 3 in, klutzy, woobie-ish little ball of pure adorkable.
- Conrad tries (and fails) so hard not to be a doormat and is such a woobie you can't not see him like this.
Most of the characters from Sakana are this, but especially Jiro, who is pretty shy in front of girls.
Rumisiel from Misfile is so cute in his complete incompetence at social interaction.
Bloody Urban gives us Angelica -the series' tall, skinny, socially awkward Unfazed Everyman.
Sabrina from Sabrina Online. She collects Transformers action figures. Her boyfriend R.C. is also Adorkable, and he collects anime figurines.
Kia the Succubus of Krakow Comics calls her boyfriend ( later her husband) her "naughty, gawky Cinderella".
Homestuck's Tavros Nitram, a.k.a. adiosToreador, is utterly dorky, and yet at the same time unbelievably Moe. Being Ugly Cute (due to being, you know, a troll) and being the biggest Woobie in the whole cast helps.
- John is another example, with reasons cited from Hussie's formspring:
Andrew Hussie: John is adorable because he is honest and heroic and nerdy and a good friend.
- Andrew Hussie himself qualifies.
- 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. In fact, pretty much all the Beta kids are this trope, Rose included once you see her silly side (eg the W magnet mustache).
Hanners from Questionable Content.
- Marigold. In a big way.
Florence Ambrose demonstrates.
Randall Munroe
Juvenile Diversion gives us Chris, the youngest, smartest, and geekiest of the protagonists. Naturally, this is why Evie is attracted to him.
El Goonish Shive got Tedd (at least, when he's not in the perverted visionary mode) and Susan (at least, when she's not in the Angry Feminist Chick mode).
Jyrras from Dan and Mab's Furry Adventures , although he probably doesn't want to admit to it.
Ryan Aberdeen from Avalon.
Gary from M�nage � 3 is one and so is Kiley. Gary is an awkward, sweet, comic book geek, and Kiley is very insecure and prone to break down crying.
King from Housepets!.
Mike from Bardsworth.
Stein from Frankie And Stein. Just... that face from page 3... there is no question of his adorkableness.
Lance and Dustin from Weregeek. Check out when Dustin was nervous about his date, and the last 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.
Heather Brown from Spinnerette could be the poster girl for this trope.
Referenced in this Wapsi Square strip.
Off-White: Clumsy Iki is a rare wolf example of this trope, depending on who you're talking to.
Chainey and PJ of Maggot Boy. Chainey is a tall skinny narcoleptic zombie and reluctant sidekick. PJ is a huge super hero fanatic with spiderman everything.
Both TJ and Amal qualify, depending on the mood. Amal's more of a modern Bollywood Nerd, while TJ just has a goofy sense of humor.
Dani and Adam from Olympic Dames would certainly count, one being a bespectacled, socially awkward( and fairly adorable in her own right) teenage girl- who just happens to be magically pregnant with a demigod; the other, 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...
Sweden and Japan in Scandinavia and the World
While many characters in Girl Genius have Adorkable aspects, it is interesting that the main three characters, Agatha, Gil, and Tarvek, are often very adorkable. This could be because adorkableness is correlated with science/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 if they're not Axe Crazy.
A few character from Inhuman qualify. Ashido and Juu Dyrano are good examples but Ro "Darkfool" Koji takes the cake. The majority of pics in his character gallery just scream "Adorkable" as well as his overall personality.
Sydney, the main character from Grrl Power
Oh, Kimiko Ross. How does a misanthropic cyborg manage to be so adorably awkward?
Charlotte of Paranormal Mystery Squad / Vampire Cheerleaders has various shades of this. 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."
Olympus Overdrive has Hades and Max.
Sunstone gives us Ally; successful self made woman, millionaire, impeccably dressed, sexually confident, sadist and complete spaz.