"The ultimate villain of the story, who's causing the problem the heroes must solve."
Note that Big Bad is not a catch-all trope for the biggest and ugliest villain of any given story. The Big Bad is the one who turns out to be behind several other seemingly independent threats.
Animorphs: Visser Three is the Yeerk enemy the Animorphs encounter the most. However, the Big Bads of the series are The Council of Thirteen, who are in charge of him. They only appear once in a side-story, and it is ultimately the defeat of Visser Three that ends the war. And then there's Visser One (the original, before he takes her position), and Crayak...
There are too many plot-lines in A Song of Ice and Fire to pick a single Big Bad; the series mostly features morally ambiguous and sympathetic humans pitted at odds with each other, making it difficult to pick out heroes and villains at all. When the Others finally come, everyone's gonna be screwed.
The Big Bad of the civil war plotline of the first three books appears to be Tywin Lannister for the most part, but in the end it's revealed the true Big Bad is Littlefinger; who is responsible for the books' main action, notably the murder of John Aryyn and the death of Joffrey.
It's hard to say for sure given the series' long hiatus, but Feast for Crows appeared to be setting up Euron Greyjoy as a Big Bad in the aftermath books, as well as Roose and Ramsay Bolton.
The Bone Season has Nashira Sargas. A nearly immortal Rephaim, she captures rare magic users known as voyants and kills them, forcing them to become her "fallen angels" which protect her eternally and from which she draws all her powers.
Castaways of the Flying Dutchman:
Obadiah Smithers in Castaways of the Flying Dutchman with Percival Bowe as Bigger Bad.
Captain Redjack Teal in the first part of Angel's Command and Maguda Razan in the second part.
Tris's Book: Queen Pauha and her mage brother, a nasty pair of type 1 Pirates who takes advantage of the earthquake damage from the first book to attack Winding Circle and its treasures, enslaving Aymery and nearly ensnaring the Circle kids as their slaves too. They cause a lot of death and destruction as well as a loss of innocence when Tris in particular gets blood on her hands to drive them away.
Street Magic: Lady Zenadia. She "adopts" a street gang to use as her personal toy because her retirement's a bit dull. She orchestrates their battles with other gangs and tries to abduct Evvy because she thinks a stone mage would be a good asset.
Will of the Empress: Empress Berenene. Unlike other antagonists, as a ruler she has many strong qualities. However, she financially squeezes Ambros in an effort to make Sandry return so Berenene can have her married off to one of the suitors she's chosen, so she can have access to the Landreg wealth. She starts this with a charm offensive on Sandry and her friends, but the claws come out when Sandry decides to leave after one kidnapping too many.
Battle Magic: Emperor Weishu. He's a ruthless tyrant who has been conquering his neighbors already in a bid to seize Gyongxe so he can claim to own the land of the gods. Briar, Rosethorn, and Evvy all leave with PTSD thanks to his atrocities.
Codex Alera plays with this one. In the first book we're introduced to High Lord Aquitainus Attis and his wife Invidia, who are the masterminds of several schemes against the Realm, aren't defeated or even directly confronted by the heroes, and keep up their role as main villains in the subsequent books. The catch — neither is the Big Bad. That would be the Vord Queen, a monster The Hero wakes up during a Side Quest early on, and is gradually revealed to be not the mindless creature she initially appeared, but an incredibly powerful and cunning adversary far more dangerous than either Aquitaine could ever hope to be. Meanwhile, Lord Aquitainus got Character Development moving him more towards Anti-Villain territory, culminating in Redemption Equals Death mixed with Alas, Poor Villain, while Invidia was pressed into service by the Vord Queen as The Dragon and died in that role.
Cthulhu in The Cthulhu Mythos series and adaptions but in the original mythos, there were a whole load of Eldritch Abominations with their own agendas, and Cthulhu was one of the less powerful. The reason why it's called Cthulhu Mythos is that he's the closes to Mankind - other Old Ones are living on other planets or dimensions, Cthulhu sleeps a few miles off the Atlantic Coast. There are some hints that Azathoth might be somehow controlling all or many of the others (even if he doesn't know it) so if there's a Big Bad at all it's more likely to be him.
The dactyl demon Bestesbulzibar in RA Salvatore's Demon Wars Saga. Rather unusually, he's defeated in his physical body at the climax of the first book; he spends most of the saga as a disembodied spirit influencing other villains, who believe they're the Big Bad.
In Dragonlance, the dark goddess Takhisis is usually the Big Bad, though at various points of the timeline she's been overshadowed by Chaos, the dragon overlord Malystryx, and once nearly by Raistlin.
Proven Guilty: We're not quite sure who sent those wraiths, but the running theory is either Maeve or Queen Mab.
White Night: Cowl
Small Favors: Nicodemus
Turn Coat: Peabody
Changes: Duchess Ariana and the Red King
Ghost Story: Corpsetaker
Cold Days: Maeve, though ultimately under the influence of Nemesis.
Skin Game: Nicodemus
That said, the driving force behind everything is the Black Council, which is believed to have been involved in setting up many of these Big Bads. Cowl is known to be a member. Nicodemus gets an honorable mention for being a non-Black Council recurring Big Bad in his own right.Cold Days further complicates matters by introducing Nemesis, a form of quasi-intelligent magical infection which takes people over and causes them to act on behalf of the Outsiders and is implied to be behind most of the various bad happenings in the series. Nemesis and its tools may or may not be the same thing as the Black Council.
In the first Faeries of Dreamdark book, it's the Blackbringer. The next book features Dusk, an old friend of Magpie's and to a lesser extent, Ethiag. Ethiag is the general (and mind-controller... person) of a huge horde of other demons, but he's still only second in command.
Firebird: Phoena Angelo is the sponsor of Dr. Cleary's biological weapons research and thus the driving force behind the invasion of Veroh, which resulted in Veroh being rendered open-air uninhabitable, the disappearance of several merchant ships, the Netaian resistence against the Federacy, and the need for Brennen Caldwell and Firebird Angelo to infiltrate and partially destroy Hunter Heights, which got them both nearly killed (by Phoena) and Brennen court-marshalled and dismissed.
Fusion Fire: Eshdeth Shirak, as the leader of the Shuhr, is the mastermind behind the Sunton massacre (utter destruction of a residential town), the attack on the Sentinel College, the deaths of the two child princesses of Netaia, Phoena's departure to the Shuhr and her imprisonment by them, Brennen's captivity after he tries to rescue Pheona on the Federacy's orders, and the plan to kill Firebird to break Brennen.
Crown of Fire: Modabah Shirak, Eshdeth's son, takes over where his father left off. He orchestrates a number of plans within plans in an attempt to re-capture Brennen, including taking over the Netaian government from the shadows and several attempts on Firebird's life.
Wind and Shadow: This book features two Big Bads, one for each thread of the story.
The Shadow possessing Tamím Bar'Baror kidnaps Kiel Caldwell, thinking him the Boh-Dabarnote a long-expected spiritual leader who was supposed to restore all people and remake the world, in an attempt to corrupt him and causes or encourages a number of destructive events, including the destruction of the planet Three Zed.
Jahana is the leader of the neo-Shuhr group and is a cruel but powerful woman. She is responsible for a number of deaths and disappearances and intends to take over the galaxy through a combination of reviving ancient technology, bringing the Shuhr policies of unlimited use of telepathy back into play, and posing Kinnor Caldwell as Boh-Dabar and using him as her spokesman.
Daystar: Piper Gambrel, along with the Shadow possessing him (a different Shadow than the above), is determined to wipe out the Sentinels. To this end, he manufacture fear and persecution of the Sentinels, forcing them all to take refuge on their sanctuary world. Once he has them thus isolated, he comes up with a way to introduce a virus which will kill them and only them, plus he has several back-up plans in place in case that fails.
Guardians of Ga'Hoole has first Kludd, and then later, Nyra. The first book had Skench and Spoorn, but they don't stick around.
Voldemort from the Harry Potter series. Each book also has its own main villain, but with the exception of the fifth, all of them trace back to or are acting under the orders of Voldemort. The fifth book's Big Bad (at least until the Ministry battle) is Dolores Umbridge, a Sadist Teacher extraordinaire utterly convinced of her own righteousness who is the series' biggest Hate Sink.
In Death series: In each book, the murderer Eve is trying to get would be considered the villain. However, for the entire series, Max Ricker qualifies as the Big Bad. Why? Well, he's a crime boss who controls a vast criminal empire. He had dealings with the terrorist organization Cassandra from Loyalty in Death. He appears again in Promises in Death, despite being in prison. Eve's father Richard Troy and Roarke's father Patrick Roarke actually worked for Max Ricker, although they were not particularly high up in the ranks of his organization. If all this does not make Max Ricker the overall Big Bad, then what does?
Like in the films, most James Bond novels have a Big Bad.
The Spy Who Loved Me: Sol Horowitz and Sluggsy Morant. Although they were both sent by Mr Sanguinetti, he is never confronted directly, and is implied to have arrested by the Border Patrol while fleeing the US.
In The Laundry Files, the overall biggest threat are the various soul-sucking horrors from beyond space-time poised to descend upon Earth once CASE NIGHTMARE GREEN goes active, and in particular the most powerful of them: N'Yar Lath-Hotep, The Black Pharaoh. However, each book has a (usually human) villain who presents a smaller and more immediate threat, who are usually taking orders from one of the aforementioned soul-sucking horrors.
Eustace 'The Evil' De Mharburg from Paul Kelly's 'The Lost Brigade'. A man so heinous that he was deleted entirely from history...
The Crippled God is this for most of the Malazan Book of the Fallen. Though not directly introduced until the third book, being The Man Behind the Man to, most prominently, the Pannion Domin, the Whirlwind rebellion, and Lether makes him the most significant and with the widest reach of any villain in the series. Ultimately subverted when after the events of book seven (when his followers lose control of Lether), the Crippled God loses most of his influence in the mortal world and the protagonists end up having to save him in the last book when a bunch of Abusive Precursors called the Forkrul Assail hijack his powers for their own purposes.
Gyphon is the overall villain of the Mithgar series. However, most of the individual books have their own Big Bads, who may or may not be trying to curry his favor, and usually come up with an enact their own schemes in the hopes of getting his support. Sometimes Gyphon's active Big Bad himself, sometimes he's The Man Behind the Man, and in other cases he's just the Bigger Bad.
Gabriel from the Modesty Blaise series is a low-key, but memorable Big Bad. After appearing in the character's first adventure, he then re-appears in ''A Taste For Death" wherein, in the words of series creator Peter O'Donnell (who was worried that a regularly-recurring villain might weaken the series), he is definitively killed at the hands of an even Bigger Bad than himself.
An impersonal example is the comet in Comet in Moominland that besides threatening to cause The End of the World as We Know It by colliding with said world causes all kinds of strange portents of doom for the heroes to contend with (ash all over the place, drying seas, storms) before it even gets there.
Petaybee: The Intergal corporation sends all of the major villains in the series to Petaybee and gets involved itself toward the end.
Ultimately, Chaos, the King of the Old Ones, is this for The Power of Five. However, he spends most of his time as an off-screen Bigger Bad while the humans trying to unleash him take the Big Bad role for each of the first four books:
Sir Michael in Raven's Gate.
Diego Salamanda in Evil Star.
Mr Chairman in Night Rise (with Susan Mortlake as The Dragon) and Necropolis.
Finally Chaos himself in Oblivion (with Jonas Mortlake and the new Chairman as Co-Dragons and Commander Strake and Field Marshall Akkad as Mook Lieutenants).
The Psalms of Isaac toys with this one. Initially, it looks like OverseerSethbert was the ultimate villain, but by the end of the first book it was plain he was a Starter Villain whose strings had been pulled by someone else. Several characters' suspicions then fall on Vlad Li Tam, but he's more morally ambiguous than outright evil, and he turned out to be as ignorant of the true cause as anyone. Then mysterious forces in the service of the Crimson Empress showed up, but she was eventually revealed to be a little girl- one raised for power, certainly, but hardly in a position to actually wield it yet. The real Big Bad appears to be the Empress's father, the ancient Wizard King Ahm Y'Zir.
The Rainbow Magic series has Jack Frost, who is always sending his goblins out to do his dirty work before appearing in the climax of a series.
Ranger's Apprentice starts off with Morgarath as its Big Bad in books one and two; the Skandians aren't really Big Bads in book three, but the closest there are to antagonists; the Temuji in book four; Keren in books four and five; the Tualaghi in book seven; Tennyson in books eight and nine; and Arisaka in book ten.
Taggerung has many major villains, with Vallug Bowbeast as the most prominent.
Princess Kurda in Triss, with King Agarnu as the incredibly pathetic Bigger Bad.
Raga Bol in Loamhedge.
Gulo the Savage in Rakkety Tam.
Riggu Felis in High Rhulain.
Vizka Longtooth in Eulalia!.
Korvus Skurr in Doomwyte.
Quean Vilaya in The Sable Quean.
Razzid Wearat in The Rogue Crew.
Brian Keene's The Rising book series has Ob, the leader of a demonic group of sort-of zombies that possess dead bodies and turn them against humankind. However, in the first book he is in a Big Bad Ensemble with Colonel Schow, the leader of an entire platoon of Sociopathic Soldiers. In the second book, with Schow dead, Ob takes his position as the true Big Bad once again.
Rogue Sorcerer has Lyr Yarika, the once-powerful lord of a noble house who has since been reduced to running a quiet little inn.
The central villain of The Runelords is essentially that universe's equivalent to Satan though it manifests in several forms throughout, including the One True Master, Shadoath, and Lord Despair.
The Inchoroi and the Consult of the Second Apocalypse series. Mostly because they apparently want to rape everything ever. And also because, according to Kellhus, the only way they can save their souls from being sent to Hell by the God is to exterminate the vast majority of the human race. The No-God is, in a way, something of a subversion of this: despite his overwhelming presence and the fact that his very existence makes every human baby stillborn, he doesn't really know what he's doing. WHAT DO YOU SEE? I MUST KNOW WHAT YOU SEE. TELL ME. WHAT AM I? Somehow, Bakker makes a Woobie out of an Eldritch Abomination.
Weekend Warriors: Doctor Clark Wagstaff, Doctor Sidney Lee, and Doctor Samuel La Fond are a Big Bad Triumvirate of dentists and rapists!
Payback: Senator Mitchell "Mitch" Webster is a Big Bad, and an HMO consisting of Elaine Monarch, Derek Monarch, and Ethan Monarch seem to be a Big Bad Triumvirate. They have seemingly no connection to each other, but apparently Mitch had sex with Elaine and got AIDS from her and gave it to Julia Webster! Hoo, boy!
Vendetta: John Chai.
The Jury: The Barringtons were being set up as this... but they got away! So the story throws in an unrelated Big Bad in the form of Domestic Abuster and National Security Advisor Karl Woodley.
Sweet Revenge: Rosemary Hershey. Bobby Harcourt seemed to be a big guy at first, but it turns out that he's just a Horrible Judge of Character who finally wised up!
Lethal Justice: Arden Gillespie. Roland Sullivan is more of The Dragon to her than a Big Bad.
Free Fall: Michael "Mick" Lyons. There are four men who are apparently subordinate to him.
Hide and Seek: Mitch Riley, assistant director of the FBI.
Final Justice: Hank Owens, with four men working for him.
Under the Radar: Harold Evanrod, the Prophet of a pedophile polygamist cult called Heaven On Earth.
Razor Sharp: Vice-President Hunter Pryce, with several men being subordinate to him.
Vanishing Act: Margaret Pearson and William "Bill" Bell, identity thieves and a Big Bad Duumvirate.
Deadly Deals: Baron Bell, with Adel Newsom acting as The Dragon.
Game Over: Strangely enough, President Martine Connor is being set up as this, but it gets subverted when it turns out that she had been reluctant to throw out Obstructive Bureaucrats that had barred her at every turn, and simply needed some urging to do it.
Cross Roads: Henry "Hank" Jellicoe, with Little Fish and Stu Franklin acting as Co-Dragons.
Deja Vu: Henry "Hank" Jellicoe.
Home Free: Owen Orzell and Jason Parker are apparently a Big Bad Duumvirate. Interestingly, Owen reveals that he was part of a Big Bad Triumvirate consisting of CIA director Calvin Span and Henry "Hank" Jellicoe. Henry is now rotting in federal prison, and Calvin is now dead from a heart attack he got while shovelling his driveway!
As indicated, Henry "Hank" Jellicoe could qualify as an overall Big Bad, especially after Free Fall.
Kingdom of the Wicked has two: Mevolent for the alternative universe and Argeddion for the normal one.
The Sovereign Stone has Dagnarus, Lord of the Void, as its Big Bad. Interestingly, though plainly the bad guy, he's also the main character; the heroes who oppose him come and go, but in the end the trilogy is concerned primarily with Dagnarus, his rise, rule, and fall note This is especially true for the first book, set several centuries before the other two, which provides the origin story for Dagnarus and his Quirky Miniboss Squad, but while he has less "face time" in books two and three, he's still more central to the story than any individual hero or group of heroes
The Star Wars Expanded Universe novels have had several. In addition to Emperor Palpatine (who usually takes the role by default during any work set during the timeframe of the movies, or is at least the Bigger Bad) some of the most notable are:
In the X-Wing Series, Ysanne Isard for the Rogue Squadron arc and Warlord Zsinj for the Wraith Squadron arc.
Thracken Sal-Solo from The Corellian Trilogy (notable among Star Wars villains for just being scum as opposed to an avatar of pure evil, and for surviving to take a supporting villain roles in later series).
Actually, Thrackan is simply an opportunist claiming credit for the actions of the real Big Bads, the Sacorrian Triad, a mysterious council that rules one of the Corellian system's worlds, Sacorria.
The Yuuzhan Vong have a whole succession of leaders throughout the series, each of whom inevitably is convinced he is/ought to be in command of the whole invasion: Prefect Da'Gara of the Praetorite, who isn't even a warrior (the title makes him a high-level bureaucrat. Seriously, no wonder he lost); Shedao Shai, fleet commander; Tsavong Lah, Warmaster, who actually is in charge of the warrior caste; Supreme Overlord Shimrra; and Onimi.
The '80s-era Lando Calrissian trilogy features Rokur Gepta, the last Sorcerer of Tund. In the first book, he tries to con Lando (whom he selected essentially at random) into finding an ancient artifact for him. When Lando outsmarts him, he becomes so obsessed about taking his revenge that he abandons his plans to subvert Palpatine's Empire to spend the next two books chasing one guy across the galaxy and making his life hell.
Galaxy of Fear is set soon after A New Hope. The villain behind all the events of the first six books is in the Emperor's employ and sometimes gets examined by Vader, but he's allowed a lot of discretion and neither the Emperor nor Vader have much of a hand in those events. So for those six books it is Borborygmus Gog who is the Big Bad. For the rest of the series our heroes are fleeing The Empire, but there's no coordinated effort to catch them.
Cleanly averted in the standalone novel Death Star. The book has no overall villain; the closest thing is the Rebellion which is at best a recurring antagonist to the Imperial characters.
In the "Bounty Hunter Wars" trilogy, Prince Xizor is the Big Bad of the flashback arc, orchestrating events to destroy the political power of the Bounty Hunters' Guild and leave a large assortment of freelance bounty hunters for the Empire's use. In the "current" arc, the Big Bad is Kuat of Kuat, CEO of the most powerful shipyards in the galaxy, Kuat Drive Yards. Kuat of Kuat is trying to kill Fett to cover up a defunct, now inconvenient conspiracy against Xizor.
The "Jedi Academy Trilogy" had several alternating Big Bads. The first book of the series had Jedi Search, and the Big Bads were Moruth Doole, administrator of the prison world Kessel, and Natasi Daala, admiral of an Imperial superweapon facility and fleet cut off from the rest of the galaxy. In Dark Apprentice, it's the ancient Sith spirit Exar Kun, who possesses a powerful but inexperienced and embittered Jedi apprentice named Kyp Durron. Imperial Ambassador Furgan also serves as a Big Bad. In the final book of the trilogy, Champions of the Force, Daala, Exar, and Furgan all serve as Big Bads.
In Darksaber, second book of the unofficial "The Callista Trilogy," the Big Bads are Durga the Hutt and Daala.
The first six books of "Young Jedi Knights," "The Rise of the Shadow Academy," the Big Bads are a cabal of rogue Imperial Royal Guards, who are manipulating Brakiss, the faux Big Bad. The next five books, "The Fall of the Diversity Alliance," feature rabid anti-Human terrorist Nolaa Tarkona.
The Big Bad of the "Jedi Apprentice" series is Qui-Gon Jinn's ex-Padawan, Xanatos, though individual books might have their own Big Bad, with Xanatos sometimes being the Bigger Bad.
For Darth Maul: Shadow Hunter, the Big Bad is Darth Sidious.
The Big Bad of the "Jedi Quest" series is Granta Omega, Xanatos' son, though like its predecessor series, "Jedi Apprentice," some books had an individual Big Bad, with Omega often being the Bigger Bad.
In The Approaching Storm, the Big Bad is a Hutt called Soergg, who is attempting to manipulate the planet Ansion into joining the Separatists, which would mean a host of planets, due to an entangling alliance, would follow with. Shu Mai, leader of the Commerce Guild and Separatist backer, might also qualify, as she is the one who hires Soergg to do this.
The Big Bads of "The Han Solo Trilogy" alternate. The Big Bad of the first book, The Paradise Snare, is the t'landa Til "High Priest" Teroenza, who runs a spice-treatment operation as a sham religious retreat. The Bigger Bad behind him is Aruk the Hutt, leader of the cartel that owns the operation. The Big Bad of The Hutt Gambit is Moff Sarn Shild, who leads an assault on the smuggling "capital" of Nar Shaddaa as a prelude for his plans to carve out his own independent domain in the galaxy's Outer Rim. It's implied, however, that the Bigger Bad is Palpatine, who used the Force to manipulate Shild in order to commit treason to give him a pretext to remove him from power. In Rebel Dawn, Teroenza is the main villain, though Han's old flame and Rebel leader Bria Tharen might count. While definitely not "bad," she tricks the smugglers, including Han, into attacking Teroenza's operation in order to seize its wealth for the Rebel cause.
The Big Bads of the "Boba Fett" series (featuring a young Boba Fett) vary. The first book lacks a Big Bad, but the second, Crossfire, has two: Count Dooku, who is prepared to kill Boba to prevent him from telling anyone that he is both the leader of the Separatists and the creator of the Republic's army, and Aurra Sing, who covets his father's wealth. Aurra remains the Big Bad for the third book, Maze of Deception. Hunted, the fourth book, features Gilramos Libkath, a small-time crime lord who uses children as his minions. In A New Threat, Wat Tambor is the Big Bad by default of being the villain Fett is hired to kill. The final book, Pursuit the main antagonist is Mace Windu.
Tatooine Ghost has Grand Admiral Thrawn as the Big Bad. Interestingly, neither he nor the New Republic realize that he's the Big Bad. He's simply attempting to purchase a piece of art, which happens to contain the communications device linking the New Republic to its numerous spies. The New Republic, on the other hand, only knows that some mysterious Imperial is trying to purchase it.
In Shatterpoint, the Big Bad is a powerful dark-side-using Force Adept called Kar Vastor.
Outbound Flight: The two Big Bads are Palpatine and the Miskara, leader of an expansionist alien species known the Vagaari.
In the first book of the "Republic Commando Series," Hard Contact, the Big Bad is a Separatist scientist named Ovolot Qail Uthan, who was developing a virus targeting Fett clones. In Triple Zero it's Perrive, leader of a Separatist terrorist cell. True Colors has no Big Bad, but Order 66 has Palpatine. Though he has no direct involvement in the plot, the characters of the series recognize that Palpatine is unlikely to appreciate Imperial soldiers going AWOL, or taking an ex-Jedi with them. 501st also lacked a Big Bad.
Darth Vader is the Big Bad of Dark Lord: The Rise of Darth Vader.
The Big Bad of Allegiance is the corrupt governor Barshnis Choard, who seeks to carve out his own independent state in the Shelsha sector.
Darth Bane is the Big Bad of the eponymous "Darth Bane" series. The main antagonists, however, differ by book. In the first book, Path of Destruction, the primary antagonist is Kaan, rival Sith Lord and leader of the Brotherhood of Darkness. In Rule of Two, Johun Othone, a Jedi Knight, is the primary antagonist. In Dynasty of Evil, the primary antagonist is Darth Zannah, his apprentice who, according to the Rule of Two he himself instituted, seeks to supplant him as Sith Master.
In Luke Skywalker and the Shadows of Mindor the Big Bad is Cronal, also known as Blackhole or Shadowspawn, an Emperor's Hand who held to a philosophy known as the Way of the Dark, a nihilistic view that stated that everything was doomed ultimately to destruction, and goals dedicated to destruction or achieved through destructive means would succeed.
The Big Bad of Blade Squadron is Admiral Jharred Montferrat, commander of the Star Destroyer Devastator, which Blade Squadron is tasked with destroying during the Battle of Endor.
In the Stories Of Nypre series we have the unnamed creature that controls the Night Land who is behind most atrocities in the series.
The Sword of Shadows series has numerous mortal villains running around, but they all pale compared to the incoming threat of the Endlords, nine godlike personifications of destruction and entropy.
The Sword of Truth has Darken Rahl in the first book, the Sisters of the Dark in the second book, and Jagang for the rest of the books, though most of those also have their own baddie for Richard to deal with, but they're almost always minions of Jagang's and the Imperial Order. The new book seems to have a villain named Hannis Arc, if the online blurbs released are to be believed.
In Those That Wake, Man in Suit is this; he can influence and control almost anyone through spreading hopelessness, and is behind several major events in the present day and backstory. The sequel, What We Become, has the Old Man, who secretly runs the world via corporate dealings and has many subordinates on hand.
Song of the Lioness: Duke Roger of Conte. In an effort to usurp Prince Jon's place in the line of succession, he calls a plague, manipulates Jon into exploring an incredibly dangerous place, engineers a war with Tusaine and tries The Uriah Gambit, tries to kill Queen Lianne... when Alanna kills him, he's actually not quite dead and one of his allies manipulates Alanna's own brother into bringing him back, and he promptly begins plotting again.
Provost's Dog: Pearl Skinner in Bloodhound. She's terrified Sir Lionel into not interfering with her at all, which hamstrings the Guard and allows her to run wild making counterfeit silver—Lionel actively prevents anyone from investigating her too closely. She also murders anyone who risks exposing her. She got the original idea from Hanse Remy, but he banked on the fact that she'd take it to an extreme.
Warrior Cats: Tigerstar is the main one. Most of the story arcs have their own Big Bad (book 1 has Brokenstar, book 6 has Scourge, series 2 has Hawkfrost...), but the majority of the time, even these characters are working for Tigerstar.
The Dark One from The Wheel of Time is the living manifestation of evil in that universe. His real name also happens to be Shai'tan.
The Winds of the Forelands has the Weaver whose real name is Dusaan. Numar also acts as a secondary Big Bad for the middle three books of the five-book series.
The Sequel SeriesBlood of the Southlands plays this one interestingly. Lici is responsible for setting pretty much all of the trilogy's bad events in motion directly or indirectly but then she dies early in the second book and the remainder of the trilogy is more a case of Grey and Grey Morality.
The Big Bad of the Young Wizards series is the Lone Power, the creator and embodiment of death and entropy. Good luck, heroes.
Isabel Kabra in the first series of The 39 Clues, Vesper One in the second.
The Marquis de Saint-Evremonde might also count, for the one chapter he's alive, anyway. Also an example of Evil Versus Evil; Madame DeFarge is one of the leaders of the revolutionaries who are going around bumping off nobles like the Marquis.
Night Probe: Henri Villon is nominally the Big Bad but he's mostly overshadowed by Foss Gly.
Pacific Vortex: Delphi Moran
Dan Brown is fond of making it seem like a huge, shadowy conspiracy is going on, when actually it's all plotted by a Big Bad — always a character who is already relevant to the plot before The Reveal — some underlings, pawns and a lot of theatricality.
From the Mistborn trilogy, the Lord Ruler is set up like this in the first book, until he's killed at the end. Later books reveal he was a Well-Intentioned Extremist, and the real Big Bad was Ruin, the dark god he'd been keeping imprisoned.
The Stormlight Archive has Odium. He might not be the Big Bad himself, but there's definitely one somewhere, and he's a pretty good candidate, considering he killed Honor.
William Shakespeare has various antagonists in his plays. The comedies tend to lack them though; if a major antagonist is present in a comedy, they will rarely be legitimately evil. note This list is incomplete. Feel free to help.