Badass Bookworm/Comic Books

Examples of Badass Bookworms in Comic Books include:

The version of Reed Richards in Ultimate Fantastic Four. His stretch powers were regarded as the suckiest of the four right up to the point where he decided to pitch in anyway. Cue Doctor Doom getting thrown into scenery, Annihilus getting shot in the mouth (with his own gun!), and Diablo getting his Supervillain Lair blown up.
Fantastic Four: The original Reed Richards at times possesses this as well. He punched out Blaastar and Klaw, beat Doom in a one-on-one time travel duel, killed a couple of dinosaurs.... He's done his bit for the cause of badassery.
Gina Diggers, in Gold Digger, recently discovered this after being the 'fish' in jail. She totally forgot that she's been, you know, hanging around superheroes without dying. It tends to work out muscles. She also has one heck of a right hook and can do the math to know EXACTLY how much it will hurt. Ancient Gina, her "future me from the past" is even more powerful, being capable of creating an entire planet.
Barbara Gordon in The DCU is one. Even when she was Batgirl, she was a bookworm who was physically unimposing and underestimated. Then as Oracle, she's in a wheelchair and still capable of kicking the ass of various muggers, five Men In Black and the elite secret agent Spysmasher on different occasions, in addition to being a master strategist with a photographic memory, unmatched computer skills and genius-level intellect, of course.
As with Batman, so too is Black Panther, with the advantage of Wakanda being more technologically advanced than either the US or Japan. To rather ridiculous levels, actually, but that doesn't stop Black Panther from being the kind of bookworm who will get back up when you shoot him.
X-Men has Sage, who explicitly has Awesome By Analysis as her superpower. Combine this with a strong Action Girl streak and you have a badass who will beat you up while explaining what you are doing wrong.
Watchmen: Although the second Nite Owl isn't as tough or smart as Ozymandius, he's still a caped crimefighter with enough technical wizardry to build his own crimefighting weapons. He doesn't look threatening, and is effectively a comic book geek living out a childhood fantasy.
Peter Parker. Science nerd. Photographer. Spider-Man. Once punched Wolverine through an unbreakable plate glass window to fall to the street 15 stories below when he was mad. Badass.
Spiderman's villain, The Shocker. Smart guy and puts up a good fight. Has updated and improved his costume and blast gauntlets based upon past encounters with Spider-Man. Also one of the most professional villains in the rogues gallery, having an alright win-loss ratio considering that he fights Spider-Man.
The JSA's Mr. Terrific is the third smartest man on the planet. He has a knack for having knacks. He also has an Olympic gold medal and six black belts.
Amadeus Cho in the Marvel Universe is the epitome of this trope. When he isn't making SHIELD look like a bunch of fools with his mad hacking skills, he manages to take down foes with pebbles because of his understanding of physics and angles. He isn't called the seventh smartest person on the planet for nothing. And it's an open question among fans whether he's really only the seventh smartest.
Tony Stark, the titular Iron Man. He also kicks ass without the use of his suit or any advanced technology, considering Captain America (comics) taught him to fight.
Tim Drake, third Robin. In a very Batman-like vein, he devotes his free time to developing electronic gadgets for crime-fighting purposes, when he's not actively trying to clone his dead friends back to life. He's been established as being way less agile than Dick Grayson, and Batgirl can wipe the floor with him (a single time when he managed to beat her is largely considered Fanon Discontinuity, for too many reasons), but he's still pretty awesome and can beat Killer Croc while having the flu.
Barry Ween, Boy Genius, is a superintelligent ten-year-old Gadgeteer Genius who often has to resort to heavy weaponry to "deal" with his failed experiments. He also Took a Level in Badass with each subsequent reboot of his series, and now he can bare-handedly wipe the floor with whole warrior tribes without even ruffling his hair. Awesomeness By Analysis certainly has a lot to do with it.
Bruce Banner is the Badass Bookworm you wouldn't want to make angry! Perhaps not 100% applicable because the Hulk is a different personality, but overall they're the same person, and can certainly scrap any of the others. Not so long ago Bruce lost his powers (again) because of Villain Sue Red Hulk. Every sign on heaven or earth shows that Bruce is so Badass Bookworm that taking away his Hulk persona can make him even more dangerous. It's easy to forget he turned into The Hulk to begin with because he had a career building super-weapons for the government, which as Banner, he's intelligent enough to use and improve upon.

Bruce: You know, it just now occurs to me that maybe the real reason I became the Hulk... was to protect the world from Banner.

- There's also the fact that not all Hulk personas are created equal. While the most commonly seen "Savage Hulk" (green) is basically all brawn and little to no brains, "Joe Fixit" (grey) is rather clever and "the Professor" (green, but more human-like than Savage) is just as smart as Banner. And then there's the Green Scar, who unlike the other personas is just as strong as Savage Hulk (if not stronger), but is also more than capable of thinking and smashing at the same time.
After a brief stint with the Wreckers in IDW's Transformers comics, during which he was badly wounded, Perceptor decides he needs to improve his combat abilities. (This takes place chronologically before his appearance in All Hail Megatron, thus retconning an answer to the question, "When did Perceptor get scary?"
Jill Trent, of the obscure Golden Age feature Jill Trent Science Sleuth, is an unusually early female version. Jill mostly relies on her prodigious science and engineering abilities to solve mysteries, as one might expect a Science Sleuth to do. But nearly every adventure ends up with Jill and her gal pal Daisy beating the crap out of the bad guys - just like contemporaneous male heroes would. (A public domain example of the feature can be seen here.)
Daredevil is a blind lawyer who just happens to be a martial arts master.
Both Dwight and Wallace from Sin City are very intelligent, well-educated men who are more than capable of bringing down the bad guys.
A certain mild-mannered reporter named Clark Kent can be quite safely stated to be one of the biggest Badass Bookworms of them all.
Doctor Strange likes to spend his free time in his study, usually in a Levitating Lotus Position about four feet off the ground. He can also take you down with a single spell or a well-placed kick, his choice.
Tintin: A highly intelligent young journalist and a force to be reckoned with. Solves crimes and punches out bad guys on a regular basis.
Lucien, the librarian of the world of dreams from The Sandman. When Dream is indisposed and the Furies begin ripping apart the Dreaming, some of Dream's more dangerous prisoners escape their captivity and try to wreak havoc. A few try to do so in the library, but those who tried didn't take Lucien into account.

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