Space Marine Librarians and Techmarines are psychics and engineers in an organisation badass down to the man; they use their extra abilities to kick even more ass.
Eldar Farseers even more so — visionary masters of lore, leaders of craftworlds, and seriously badass fighters. Now compare them to the Great Harlequin, the leader of the race's organization of historian-librarian-bard-acrobat-ninjas who are some of the most feared close-combat specialists in a game that already turns everything Up to Eleven.
Any Champion of Tzeentch would be one, to say nothing less of the master of change himself. Notably Ahriman is both an extreme bookworm and can kill a Monstrous alien with one smack of his staff.
And Adept Castus Grendel from a game session report, who made it into canon. As non-melee oriented character as they get, who tried to delay a major daemon for a round (the question was already not whether PC can win, but whether they can take it with them) and on a good roll decapitate it with one strike of a common knife. And later made a star career on killing ridiculously powerful daemons.
Don't forget the Emperor of Mankind. This is the guy who personally engineered the Space Marines and a lot of other stuff, including: planning the renovation of the Golden Throne and the Empire's beachhead in the Warp to try and get access to the Old Ones' Webway (which was inherited by the Eldar) with the aid of legions of Adeptus Mechanicus. Granted, this is to be expected from someone with at least 30 millenia of time under his belt. A self-proclaimed atheist and a really big supporter of science and its progress.
What about Inquisitors. These are the guys who are supposed to root out, study and purge all threats to mankind whether within or without and often are very good at taking to the battlefield themselves alongside the Ragtag Bunch of Misfits that they have recruited from all over the place.
In fact one could consider the Inquisitors as being the 40k equivalent of Commander Shepard.
As far as tabletop games go, the wizard class (or magic-user, in the older versions) is probably the oldest example. Raise your hand if you can wish for something and have it come true. See this motivator. One should always remember the primary rule of Epic Levels and Forgotten Realms. "Beyond level 20, you should listen to the wizard." Epic monks can shatter castles with their fists. Epic wizards can shatter planets with a couple gestures and some words.
Similarly, Archivists and Cloistered Clerics (the divine bookworms) can cast Divine Power to transform themselves into beefy bruisers.
There is a feat called Knowledge Devotion which allows one to translate knowledge about a given creature directly into more accurate and powerful attacks against that creature. Numerically, the potential benefit rivals the most powerful non-epic weapon enchantments.
Third edition Bards are fantasy Indiana Joneses. In addition to decent fighting ability, they get the Bardic Knowledge ability. For class skills they get Appraise, Decipher Script, Gather Information Spellcraft and Use Magic device; all of the "knowing skills". They are also the only other base class that has every knowledge skill as a class skill. A successful Knowledge check gives the character (not just the player) meta-game knowledge of a creature's stats, giving the player a huge advantage in combat. And they have Whip Proficiency!
Dark Sun bards may have this beat; they preserve all forms of knowledge and tradition, including poisons and martial arts, making them less minstrels and more assassins.
Bards are also the only core class with Speak Language as a class skill; all other classes in the core books (there are a few others strewn around in other books) aside from (depending on skill selections) NPC class experts have to gain additional languages as a cross class skill (meaning it takes twice as many points).
The GURPS Black Ops RPG setting features an organisation of Badass special ops/MIBs, with two divisions filling the Badass Bookworm category: the Science division (multidisciplinary scientists) and the Tech division (engineers). The former usually knows medicine and how to best fix or take apart the human body, while the latter can build ultra-tech (if unstable) superweapons.
The Ordo Dracul in Vampire: The Requiem throws themselves into this trope. The Sworn of the Axe, the "militaristic" faction of the Ordo Dracul, are Badass Bookworms par excellence. For the "goon squad" of the covenant, the Sworn of the Axe is nevertheless filled with geniuses, mad scientists and librarians... all of whom are dead fascinated in mowing over anybody that stands in the way of Transcendence from vampiric existence. However, the Ordo Dracul's founder, Vlad Tepes, subverts this trope quite a bit, though; Vlad starts out as Vlad the Impaler (yes) and it takes him 200 years to get to the point where he can read. Then he goes on to become the Vampire L. Ron Hubbard.
The Mysterium (Mage: The Awakening), meanwhile, has been in steady existence since the fall of motherfucking Atlantis. It's been hinted at fairly regularly that the Mysterium could have Awakened the whole of mankind a dozen times over, but they choose not to, if only because they are the librarians of the secrets of everything, and nobody comes to understand anything about the real universe unless they pay homage to the Mysterium first.
The Free Council from the same game also have elements of this. A good chunk of them are scientists, social engineers, and other nerds who want to poke the established order of things with a stick. However, they've also got their share of freedom fighters who are willing to die for their personal cause, and one of their personal tenets is "Destroy the followers of the Lie." In fact, the Order first came together when they were simply a group of banded together Apostates who were offered power and control by the Seers of the Throne... and promptly responded by cementing their bonds and killing every Seer they could find.
Also, innumerable hunters in Hunter: The Vigil also fall into this flavor, including the Loyalists of Thule (ex-Nazi occult researchers turned to killing the bad things and trying to atone for World War 2 being their fault) and the Null Mysteriis, who blend the Badass Bookworm with the Sufficiently Analyzed Magic.
The Autumn Court from Changeling: The Lost are also this to the degree. They're the ones who are most typically focused on finding out just how far fae magic goes, so they're the ones who study the Hedge, look into the origins of Contracts, and gather as more occult wisdom and lore as they can. But all courts have a guiding emotion. Theirs? Is fear. Which means they have powers that can make you wet your pants with a mere gaze.
The Order of Hermes from Mage: The Ascension are perhaps the magical researchers par excellence, having spent centuries studying magic and creating spells. At least two of their Houses - House Flambeau and House Tytalus - translate that wealth of magical knowledge into taking down the Order's enemies.
The Sons/Society of Ether take a different tack, studying magic through the perspective of Awakened Science in order to improve the world. For a number of Etherites, that means turning super-spy, Adventurer Archaeologist, or just straight-up pulp hero.
The Virtual Adepts, meanwhile, use information technology as the focus for their magic. Beware the computer geek who can hack reality.
No small number of Technocrats would also qualify, notably members of the New World Order, Progenitors, and Syndicate.
Most any blood magician from Vampire: The Masquerade, not least the Tremere clan, a former House of Hermes that turned to vampirism.
The Arcanum are the major Badass Bookworm faction of the oWOD's hunters, devoted to the investigation of esoteric lore.
Meet the Twilight Caste from Exalted. They are engineers, scholars, and lore-keepers; the original signature character, Arianna, Exalted while trying to interpret a particularly tricky poem. They are also the ones most likely to design a BFG powered solely by the flow of the universe and unleash the kind of sorcery that can scythe entire battlefields clean.
They were also largely responsible for exiling the Primordial Malfeas to Elsewhere, and then sealing a whole bunch of Yozis (plus every demon in Creation) into him - effectively, they created Hell. The "scythe entire battlefields clean" spell is aptly named "Total Annihilation", the magical equivalent of a tactical nuke - and it's far from the only one. There is also the Light of Solar Cleansing, not to be confused with Cleansing Solar Light - killing all "creatures of darkness" (doing severe damage to bosses) within 5-10 miles from the caster. And if you are smart, you can use a Crucible of Tarim to bottle spells for future use...
Their cousins, the Daybreak and Defiler Castes, are also this, which is unsurprising given they're based on Twilight Exaltations. As of setting start, they've only been around about 5 years, so they haven't had the chance to match the Twilights' full scope... yet.
Anne Marie in A Touch Of Evil is one, as she gets an increase in her Combat skill for each book in her possession.
Rifts has the Rogue Scholar and Rogue Scientist classes. They are seekers of lost knowledge and Lost Technology, dedicated to uplifting the masses and learning all they can. However, Rifts Earth being the Crapsack World it is, they can also handle themselves in a fight, with weapon proficiency and hand-to-hand skills being part of their starting package of skills.