Adorkable/Fan Works

Dungeon Keeper Ami has Empress Mercury who certinly counts, especially with the frequent Mad Scientist gag. From a fifteen-year-old it's very much so.
A lot of Prince of Tennis fanfiction involving Kaidou Kaoru involves him being like this in a relationship. Well, the ones that don't pair him up with Momo... Those are pretty much Belligerent Sexual Tension with Kaidou as Jerk with a Heart of Gold and Momo as a male Type B Tsundere.
The State-tan Project (A collaborative Fan Work for Axis Powers Hetalia) has Mississippi, Wisconsin, and California.
Ignoring their Creepy Child shenanigans, both Kaworu and Kei (female example) can come off as this in Nobody Dies.
Wheatley in the Portal 2 fic Test Of Humanity after becoming a cyborg (GLaDOS implanted his "brain" into a human body For Science!). Tall, nerdy-looking, clumsy, noticeably chubby, yet friendly and well-meaning. Even Chell admits she finds his awkward nature to be endearing and it's part of the reason she falls in love with him.
In the fanfic Blue Sky (Also a Portal 2 fic)the Ridiculously Human Robot and his once human self, Wheatley is portrayed this way. Being 6 feet 7 inches tall, lanky, clumsy, goofy, sweet (at his better moments), wears glasses, and is bound to go off on many many monologue style tangents.
tecnicianMagician and constantThinker in the Homestuck Fanfic Adult Stuck.
Princess Luna...in socks!
- Twilight makes a snowmare.
Female example: Xanatos, a Death Note fanfic, gives us Linda, whose awkward stuttering and occasional shyness are just all too endearing.
- From the same fanfic, Near is this when he carries on a phone conversation.
The nerdiness of the My Little Pony Friendship Is Magic characters Twilight and Luna gets dialled up to about fifteen in the fanfic Too Intelligent to be Loved, and it is adorable. Let's put it this way: in chapter 5, Twilight decides to throw a "science party" with events like Guess-That-Mold-Culture and All-You-Can-Titrate. Luna is so enthused at the prospect she begins spouting seriously out-of-date, badly mishandled slang that she learned from a book entitled "1001 Idioms and Colloquialisms".

Luna: This is great! We cannot wait! Astronomical Observations! Telescope Calibration! And Trivia Pursuit! This should be a detonation! Is that the right wording? This should be a detonation?

Celestia: ’This should be a blast’ is more commonly used.

- The Cutie Mark Crusaders' show was so cute and awkward!
Caramel of Assumptions becomes this trope whenever an attractive girl talks to him directly, constantly stuttering and flubbing his lines. Ironically, his main love interest grows fond of him since he doesn't act differently around her, though he does regress back into this after a few teases from her.
Adam Squall, the Author Avatar of Rise of the Galeforces, if his official artwork is anything to go by. May Niobrara have mercy on your poor soul, however, if you call him a "dino saur."