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 forgot that she's been, you know, hanging around superheroes without dying. It tends to work out muscles. She also has 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 a planet.
Her villain counterpart, The Calculator, was rebooted as one of these. He is even able to outwit Batman himself as a knowledge broker.
X-Men: 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.
Also Kitty Pryde. Not only is she an electronics genius as a teenager, but she then gets ninja training from Wolverine and develops her phasing power so that she can hit you whilst she's phasing through somebody else.
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. The epitome of this trope due to being the first known teenage outcast super hero. He's the master of this trope because, despite being a nerd, he gets all sorts of awesome powers and is a straight up Chick Magnet. Second only to Tony Stark in that area (also a fellow Badass Bookworm), but Parker is the original Nerd Superman.
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 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.
Bane is a good villain example. In prison, he spent nearly all his time reading tons of books, learned six languages and educated. All while training himself.
And Static is certainly no slouch in this area either. He's a science nerd who happens to kick plenty of metahuman ass. His methods are often very simply effects that are accomplished through impressive knowledge of physics and electromagnetism.
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 SueRed 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.
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. He does this by adding gyroscopic stabilizers to his arm, an advanced targeting visor to his head, and a bunch of other upgrades that have the end result of turning him into a brutally effective Cold Sniper. (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.
Tintin: A highly intelligent young journalist and a force to be reckoned with. Solves crimes and punches out bad guys on a regular basis.
Professor Calculus. Who would have thought that the meek-looking stereotypical absent-minded scientist is a savateur?
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.
Thessaly as well. She's a several-thousand-year-old Greek witch who's first introduced as Barbie's nerdy neighbor. She then kills a man, forces his spirit to come back so she can interrogate him via his face which she cut off his skull and nailed to a wall. She then goes into the Dreaming to help Barbie. In "The Kindly Ones" she tracks down Lyta Hall, brews a potion and kills a lamb to protect her. After Lyta comes to she sees Thessaly reading a book and warning her a lot of people are angry about what she did. Thessaly calmly warns her to run, because those people want revenge. And Thessaly's one of them.
Barry Allen, whose powers also come with the benefit of giving him a faster working brain, and were caused by him playing with chemicals. He's one of the most powerful superhumans in The DCU, but he's also a scientist by trade.
Bart Allen is more of a Cloudcuckoolander by personality, but he may qualify for this trope on a technicality for using his super-speed to read every book in the San Fransisco Library in a single afternoon. Since then, his usual 'wing it' strategy has been interrupted by occasional bouts of scholarly tactics.
Mockingbird, AKA Dr Bobbi Morse, was originally a biologist and SHIELD researcher, until Nick Fury decided she'd make a great spy and trained her. She's since became one of the most badass, if undersated, Avengers around.
Then there's Norman Osborn, who took a drug to boost his own intellect, becoming insane and super strong in the process. His successors (his son Harry Osborn and Roderick Kingsley, the first Hobgoblin) followed suit.