The main heroes in Greystone Valley include two children, a mouse-sized dragon, and a very pessimistic warrior. In a world populated by fey, dragons, and wizards, this motley crew still seems to be the best hope of saving the day.
Skulduggery Pleasant has a well-dressed living skeleton Deadpan Snarker (who is a detective), a teenage girl with odd heritage who owns a mansion, a beautiful blonde woman with a sword who kills things for a living, and a heavily-scarred tailor who is also a boxer. They are later joined by the last teleporter, a vainglorious teenage boy with excessively stupid hair. All of them are mages. None of them are remotely normal. And in the fourth book, Billy Ray Sanguine actually refers to the protagonists as a "Motley Bunch of Misfits" or something along those lines, but of course, the writer is One of Us.
The group designed to free Ciri in The Witcher was ultimately formed from an aged and mostly retired monster hunter, elder vampire, amazon bowwoman, perverted bard, teenager with villainous background and friend-turned soldier/secret agent/noble from the hostile empire. Also, few times a half dozen or so dwarves were thrown in.
Monstrous Regiment features one of these. Not only does the titular group of Borogravian soldiers qualify, they're all secretly women in disguise. The Monstrous Regiment's survival is a little more believable when you take into account that several of their number have super(natural) powers and their commanding officer (in fact if not name) is a Magnificent Bastard who knows everyone on both sides of the conflict and carries a bit more pull than you'd expect a sergeant to have. It may have helped a bit that they thought the enemy's senior commander was Vimes and he was gunning for them. But Vimes was not the enemy commander, Ankh-Morpork was not directly part of the fight, and Vimes is very pointedly not military; he is a policeman. But his help was very helpful.
And of course, the early City Watch novels. The change occurs after Feet of Clay, when the Watch starts getting so big that Vimes doesn't even know all his officers anymore. (Vimes still thinks of them as being something of a ragtag bunch, of course—no one sane wants to be a copper.)
Just as big a bunch of misfits are the night watch in Night Watch.
The witches are also somewhat of a bunch of misfits.
For a non-Discworld Terry Pratchett example, the titular group in Nation, made up of the remnants of many different Polynesian tribes who have managed to survive a tsunami and attacks by the Raiders, led by a Flat Earth Atheist teenager whose tribe was eliminated before his initiation ritual into adulthood could be completed, meaning that to the others (except Daphne) view him as basically having no soul and being possessed by a demon.
Knowingly enacted by a Genre Savvy warrior in Mercedes Lackey's Tales of the Five Hundred Kingdoms series. An ambient magical force in the land (The Tradition) likes to have events work out like they do in stories. The warrior assembles a group of untrained teenage girls, equips them to look suitably ragged, and leads them into battle. The Tradition then ensures that they fight like expert soldiers, because they qualify and Underdogs Never Lose.
The Wraith Squadron novels in the Star Wars Expanded Universe were based on this principle. Having witnessed some of the problems his squad ran into during the Bacta War, Wedge Antilles proposed a new type of squadron. To address the New Republic's budgetary problems, he said that he would give the squad to them "for free"—taking the washouts, the disciplinary screwups, the mental cases, aliens who just had trouble fitting in with human and near-human societies, and those who were in general on the verge of being discharged, to get them out of other commanders' hair but still give them one last chance. During the initial interviews and subsequent training missions, Wedge did wash out those who were truly irredeemable—those who were obviously emotionally unstable or had criminal tendencies, among other faults. He was shooting for a roster of twelve—a full squadron—but only ten of the approximately fifty applicants made the cut; the remainder still fit this trope very well.
After Wraith Squadron's initial success, though, several new members explained that they signed up because of the squadron's success rate, unaware of their initial reputation. That being said, they are either as charmingly wacky or as deeply scarred as the original squad, and soon fit right in. The Wraiths are eventually considered competent...if unpredictable, unorthodox, and hardly military disciplined. Appropriately, they're recommissioned as an Intelligence unit.
Rogue Squadron isn't exactly what you'd call orthodox either; although they're not as wide out as the Wraiths, they sit somewhere between the Wraiths and the regular military.
It seems this makes up most of the Malazan Empire's army. Well at least the Bridgeburners and the Bonehunters anyways.
It's hinted that the Empire actually encourages that sort of thing, believing that allowing individual squads (and soldiers) to find their own idiosyncratic ways of fighting is more efficient than enforcing conformity in the ranks. Seeing as this is more or less accurate in the Heroic Fantasy world the story takes place in, this might make the Empire an entire nation that is Genre Savvy.
And then there's the Mott Irregulars, a bunch of insane country hicks lead by twenty warlock brothers and a sister (the meanest of them all) who are so ragtag and fit so badly that they managed to run circles around the Bridgeburners for more than a year and win at the end.
The Phule's Company novels have this as their premise; The "Omega Company" is a dumping ground for troops that no commander wanted to deal with, and Phule is given command as a punishment for strafing a peace treaty signing. Naturally, the Omega Company just need a leader with charisma, patience, flexible ethics, and loads of money, which is what they get in Phule. The rest goes splendidly.
Justified in Eve Forward's Villains by Necessity, where only criminals and evildoers can save the world, and there's only a handful left. Naturally, it takes a while for them to get along.
The 27th Penal Panzer Regiment of the Sven Hassel novels is made up of ex-convicts and court-martialed soldiers who have been 'pardoned' and sent off to die for Nazi Germany.
The Zone series of World War III novels by James Rouch is about the Special Combat Group, made up of soldiers picked up on their various assignments from the US, British, and Dutch forces, and deserters from the Soviet army and East German border police. The established special forces units despise such ad-hoc groups and are exerting political pressure to shut them down.
In Dan Abnett's Eisenhorn novels, Inquisitor Eisenhorn's retinue includes in their number: a gunslinging pilot, an aging scholar who's literally addicted to knowledge, an ex-cop, an anti-psychic prostitute, and a flamboyant cyborg starship captain. And that's just the first novel.
In Dan Abnett's Ravenor novels, Inquisitor Ravenor, though starting with a retinue, adds a Street Urchin, an arbite who was targeted by the Chaos forces for knowing too much, and a doctor who is working illegally because of having lost his license by caring for people not allowed to be treated and falsifying records to get the supplies he needs.
Sandy Mitchell's Dark Heresy novels have the Angelae Carolus, comprising among their number an ex-cop, a fanatic assassin, a cyborg who spends a lot of time contemplating the oddness of human speech patterns, a pair of Imperial Guardsmen who just happened to be in the wrong place at the wrong time, and Inquisitor Carolus' former pyrokine girlfriend.
The Wheel of Time series has quite a few examples, though it's usually a mix of Badass and misfit. Perrin and his band of Two Rivers men, Cha Faile, the rebel Aes Sedai, The Kin, and especially the first band of main characters in the first book.
In Sandy Mitchell's Ciaphas Cain novel Duty Calls, Inquisitor Vail's retinue already includes a former commissar/member of a penal regiment, and a former arbite who had, while undercover, imploded a criminal organization with a judicious murder and frame, and picks up a food vendor who had stumbled into some knowledge of the Inquisition and picked up a gun when cornered by a Chaos cult. Warhammer 40,000 Inquisitors seem to attract this trope. It's lampshaded, too; Cain wonders if eccentricity is a requirement for joining up with Vail, who notes that in a job like that, you just tend to find more people whose view of the universe is... unusual.
In Death or Glory, Cain whips together "Cain's Liberators" from the tattered remnants of the PDF armies and civilians on the continent overrun by orks. Including getting all their medical attention from a vet.
In For the Emperor, the ragtag band of court-martialed soldiers offered amnesty in exchange for their services function as a well trained military unit. So much so that even two of them who were specifically court-martialed for trying to kill one another were able to work together without incident... at least between each other.
Gav Thorpe's Warhammer 40,000Last Chancers novels fit this trope to a dark and bloody tee, being made up of the scum and villainy of the Imperium.
In Sandy Mitchell's Warhammer 40,000 novel Scourge the Heretic, Carolus already has an interesting collection in his retinue, consisting of a sanctioned psyker, a former policeman, a psychotic fanatic assassin, and a tech-priest. He picks up two soldiers who were at a post when witches attacked and alerted him, and the shuttle pilot who took him there.
Poul Anderson's Operation Chaos ends with the narrator considering the ragtag bunch of misfits that had literally gone To Hell and Back. He concludes that it's the devil who has no sense of humor; God must love to laugh.
In Tad Williams' Otherland series, the group of protagonists that ends up infiltrating the Grail Brotherhood's private virtual reality network consists of a South African schoolteacher, a Bushman, a pair of American teenage gamers (one of whom has a terminal disease), a third teenager who's an ex drug addict, a reclusive blind French researcher, a Chinese grandmother, a German doctor and cult refugee, and an old man who's an Accidental Pervert. Their only connection is that they all know someone who's fallen victim to the mysterious comas caused by the Other and stumbled upon the clues left by Mysterious Informant Sellars.
In Temeraire book five Victory of Eagles, the title character forges one of these from the collection of renegades, retirees, and rejected experimental crossbreeds that were in the dragon breeding grounds he was exiled to, after getting word that his captain had been killed and Napoleon had invaded Britain.
The Night's Watch consists largely of outcasts, petty criminals, and political refugees and (surprisingly) even allows the overweight to join their ranks. This makes it all the more of a combined Crowning Moment of Heartwarming and Crowning Moment Of Awesome when the fat Samwell Tarly slays a seemingly invincible monster.
The defense of The Wall in A Storm of Swords takes this trope Up to Eleven. Since most of the Watch's best men have been killed, and the best of the rest are engaged in fighting elsewhere, only the very bottom of the barrel and some volunteers from a nearby town are left to fight the Wildling horde.
The Brotherhood Without Banners, made up of the remnants of a royal mission for a now very dead king, as well as a collection of miscellaneous stranded soldiers, armed peasants, petty bandits, and the like. It's telling that both of their leaders have been Westeros' equivalent of zombies
There are two in Michelle West's The Sun Sword/House War series. The first is the army of the Kalakar, the Ospreys. The second is Jewel's den, which are the much more ragtag bunch of misfits that are significantly more badass. Granted, they have an overlapping character who provides a liberal dose of overkill, but both fit this trope.
In the Farsala Trilogy, the entire Farsalan army is this after the defeat of the deghans in the first book, Fall of a Kingdom.
The investigating team in The Alienist matches this description.
In Dale Brown's Act of War, Task Force TALON starts as a mish-mash of FBI agents, "lab-bound mavericks" and actual combat-hardened personnel.
Animorphs: The only defense the human race has against a race of parasitic aliens who take over their hosts' brains and render them completely helpless? Five teenagers and an alien cadet.
Everworld has this even more. Especially in the later books when the stakes are higher and Senna gets more antagonistic.
The Chosen Men under Sharpe in the Sharpe series of books by Bernard Cornwell. They are not vastly different from most infantrymen (the recruitment procedure was very loose back then) but their flamboyant personalities and lackluster approach to discipline makes them this very trope. They are scorned by officers but tolerated by pragmatic commanders like Wellington or Hogan who tend to highly value the unit's combat prowess and experience.
In Romance of the Snob Squad by Julie Anne Peters, the Snob Squad is one of these. Jenny is overweight, Lydia talks too much, Max is big for her age, and Prairie only has one leg. They end up together in a P.E. class competition. They end up subverting the Underdogs Never Lose trope and losing the competition anyway, and Jenny even comments on this, saying that "if you think we pulled ourselves together and won this thing, you've OD'd on Disney".
Implied in the Percy Jackson and the Olympians and The Heroes of Olympus series. Because of their natural battle reflexes, amplified senses and hardwired-for-ancient-languages brains, demigods in the mortal world are usually diagnosed with ADHD and dyslexia, so they tend to be isolated from other kids, and since, apparently, most teachers are monsters, they tend to fail in school a lot. The main protagonist and narrator of the first series, Percy, has been kicked out of almost every school he's ever attended, to the point where the only time he wasn't, he joked that he'd have to try harder to keep the record, and it's implied that he's never had many mortal friends. Many demigods share similar stories. Yep, these are the kids who hold the fate of the world in their hands.
Raymond E. Feist's Shadow of a Dark Queen book of The Serpentwar Saga has a bunch of convicts sentenced to death by hanging, given express (but effective) military training and sent on a suicide mission across the ocean, on the condition, that they may be given pardon, if they succeed and come back alive.
In The Dresden Files, any time Harry brings along more than one or two people to help take on the book's bad guy, it's this. The biggest so far involves his assault on the Red Court at the Chichen Itza. Aside from a snarky wizard, his attack force consisted of his teenage neuroamncer apprentice, an agnostic paladin wielding a holy sword, a Chicago PD lieutenant also using a holy sword, a spirit of intellect locked away in a skull, a half-vampire journalist, a White Court vampire, a fairy noble, a vampire hunter, and a temple dog.
In Rainbows End, the Library Cabal, who are ostensibly trying to stop the destructive digitization of the library's contents. They don't even know they've been recruited by The Rabbit to try to save the world.
In one book of Fiona Patton's Tales of the Branion Realm series, a child ruler is on the run from traitors who assassinated her father and now control the guards and priests who are supposed to be protecting her. For bodyguards and advisers, she instead has a family of artists, a troupe of traveling actors and tumblers, and two of the (repentant) traitors. The group hails from three different countries and two opposing religions.
In the Destroyermen series by Taylor Anderson, the actual Destroyermen are described as this. They're even called the misfits of the navy clumped together in the Asiatic fleet because they fit no where else and were even called a ragtag group of misfits in the first book.
The crew of the first U.S.S. Excalibur in Star Trek: New Frontier was definitely this: the Captain was a former rebel leader who overthrew his planet's oppressors when he was twenty and spent the last few years working Black Ops, the chief engineer is from a race of hermaphrodites, the CMO is harboring the katra of her lover who died during ''pon farr'', the science officer is hiding the fact she's half-Romulan, the helmsman falls asleep at his station...the most normal of the bunch are Commander Shelby and Ensign Lefler (both imports from Star Trek: The Next Generation), and even they're a bit off.
Nuke's team in Codename Omega by Jessica Meats definitely count. You've got a physics genius who's next to useless in combat. There's an upper class psychology student who likes beating up bullies. There's an English literature student with a passion for martial arts. There's a pair of teenagers, one who'll shoot before he thinks and the other who is training as a medic. All led by a mysterious guy with no name who might or might not be human. It doesn't get any better when they're joined by an inexperienced security guard who learned to shoot by playing laser tag.
The Bronze Barbarians from the Prince Roger-series downplay the trope by way of Bunny-Ears Lawyer. The Barbarians insist that all new recruits be not only incredibly badass, but also possess some potentially valuable skill other than shooting things and polishing parade uniforms. This leaves you with people like the shipbuilder's apprentice turned armorer who uses more curse words than punctuation marks, the Master Sergeant who is also an accomplished dressmaker and an ordained Satanist priestess and the support gunner who joined the Army in lieu of doing time for car theft. The Bronze Barbarians are by no means ragtag, but they do snag up some... interesting people.
Andrei Livadny's Tsar Gorokh's Detective Agency series has the titular agency composed of a Fish Out of Temporal WaterBy-the-Book Cop, Baba Yaga (a forensics and magic expert), a young peasant man named Mit'ka (who mixes Mother Russia Makes You Strong, Dumb Muscle, and Large Ham), Yaga's black cat Vasiliy (who appears to be smarter than most people and may or may not be a Talking Animal who prefers to stay quiet), Sotnik (Lieutenant) Foma Yeremeyev who commands the hundred streltsy (guards with Hand Cannons) assigned to the agency, the later addition of the Azerbaijani domovoy (house spirit) Nazim (who has the hots for Baba Yaga) with the occasional assistance of the Tsar himself (when he wants to play detective) and, in the final novel, the cop's fiancée (a former demoness) and Tsarina Lidia (the Tsar's Austrian wife who doesn't mind the occasional manual labor much to the horror of the nobles).