Badass Bookworm/Web Comics

Examples of Badass Bookworms in Web Comics include:

Nearly every educated Spark (mad scientist) in Girl Genius qualifies for this Trope, including the protagonist, Agatha. Not only can they build death rays and turn even the most innocuous of mechanical items into death traps (such as a merry-go-round that can level a small town), but they are generally shown kicking butt with their bare hands (and feet) as well as with less sophisticated weapons, such as giant wrenches and rapiers. And don't forget brooms! Badassness depending on anger level seems to be common among sparks.
Both Narbonic and Skin Horse have more than enough Badass Bookworms to satisfy even the most jaded troper. If Dave from the former isn't the very CHARACTERIZATION of this trope near the end, well.
Dr. McNinja. Totally badass. Has an MD.
Axe Cop: Uni-Man. He comes from a planet whose collective intelligence caused a mutation in the planet itself, and is himself a brilliant scientist, currently developing powerful weapons for Axe Cop and his team. However, when Dr. Stinky Head steals his unicorn horn, Uni-Man interrupts the ensuing carnage to reclaim his horn...and then this happens.
Vaarsuvius from The Order of the Stick is an excellent example.
Zaebos from Earthsong is a member of the elite Haven Guard, and the librarian.
Schlock Mercenary
- Captain Tagon usually wears epaulet grenades. Kevyn Andreyasn "I'm not a Mad Scientist" used to wear a tank killer (shield-breaching) grenade floating over one shoulder and 13,75 kiloton yield antimatter bomb over another.

I am Commander Kevyn Andreyasn , I have shaped the destiny of worlds, of nation, of galaxies. I have created and destroyed. I have followed and I have led. I flirt with death for a living and I have cheated with the reaper more time than I can remember.

- Also, Para Ventura can pull some showy daring feats when she doesn't freeze in fear, Doctor Bunnigus, Reverend Theo, the company's lawyer Massey, Ennesby, and probably a few others.
Colin from Goodbye Chains. Attended MIT with enough engineering skills...to blow everything the shit up. Oh, and guns. Can't forgot those.
Keychain of Creation: Misho. Dear Gods in Yu-Shan Misho. Now being a Twilight Caste Solar is all about being a Badass Bookworm in the first place, but Misho is a glasses-wearing healer who prefers to use Awesomeness By Analysis to defeat his foes. And if you piss him off, he will obliterate you.
Felicia Whitewind from Fetch Quest: Saga of the Twelve Artifacts also qualifies, since not only is she a scholar, she's also capable of making it hard for thieves to get to her. Just watch her and you'll see.
In Jill Trent, She-Sir Science Sleuth, a parody Remix Comic of the original Jill Trent Science Sleuth feature, Jill fights like the man she once was, but thanks to the wonder of Femavium, her girl-brain cells now have the proportional density of 58 girls! Perfect for Doing Science!
Benjamin Hewitt, protagonist of Bibliography qualifies.
Joey from Opey the Warhead. Complete with Berserk Button that turns him almost Axe Crazy. Thankfully Opey snaps him out of it.
Dexter from Powerpuff Girls Doujinshi is able to fight on even terms against the Powerpuff Girls with his robot backpack. Also, in later chapters he fights in hand to hand combat against his rival Mandark.
Alexander Hamilton and Nathan Hale of The Dreamer definitely qualify.
bookwyrms is about some female students in a magic academy who work in its library in retrieving ancient lost tomes. To quantify their power, the demigoddess isn't the strongest one (despite displaying Hercules levels of might)
Nan in Lovecraft Is Missing is a librarian who also happens to be an expert in the occult. Considering this is a Cosmic Horror Story based on the works of the Master Himself, that's not exactly a field for the fainthearted. Luckily, Nan is a highly effective ass-kicker who faces thugs and Eldritch Abominations with equal aplomb.
Ayanah from Pawn. A physically weak scholar type, she uses her considerable smarts to traverse a legendary dungeon that claimed the lives of mighty warriors, stops the demon guardian from killing her by reciting an obscure demon law, beat said guardian by challenging her to a game she knew the demon knew nothing about, and effectively enslaved said demon with a kiss.
Bob of True Magic, pictured above. He later threatens somebody whilst the sword's still in the book.
Rose from Homestuck is constantly teased about her reading material by the other kids, which is heavily weighted on the goth and fantasy side of things. Upon entering the Medium, though, she uses that knowledge to become a powerful witch, or something very like it.
xkcd to the forces of darkness: remember that sysadmins are obsessive people who played way too much FPS.
Zokusho Comics: Jack's a mage and apparently plays chess quite well. He also sets people on fire.

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