"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.
Berserk mainly has the Godhand, and Griffith post-Face-Heel Turn in particular, as Big Bads, but several arcs of the manga have seen Guts going against other servants of the Godhand. The Lost Children arc had Rosine, and the Conviction arc had Bishop Mozgus, with the following arc focusing on Emperor Ganishka. The worst part? They only exist because humanity subconsciously wants a Big Bad to blame for their suffering.
Sosuke Aizen is behind almost everything that's happened in this manga. Even in the final arc where he's technically still in prison, it turns out he's somehow involved in events and he's even manipulated Yhwach after only a few moments of contact. How and why he's involved, however, takes time for the arc to reveal. Aizen is so ensnared in the events of the manga that it's ultimately revealed that the only reason Ichigo and Uryu were conceived was because of him, since his actions are what caused Isshin and Masaki to meet.
In the final arc, Yhwach, The Emperor of the Vandenreich, is revealed to be involved in almost everything Aizen isn't. This includes the existence of the Quincies and the Great Offscreen War with the Shinigami. He also caused the deaths of Yamamoto, Ichigo's mother and Uryuu's mother, and formed the Vandenreich. Shutara claims he's more evil than Aizen.
In Chrono Crusade, Aion's behind a huge chunk of the bad things that happen and is the final foe Chrono and Rosette have to face—although in the manga his morality is a little more gray than his anime counterpart.
Charles zi Britannia of Code Geass is a subversion. He's advertized as the prime villain, but he's generally inactive except for a couple episodes (which you can literally count on one hand).
Combattler V: Empress Janera, even though she was working through pawns for the first half of the story.
Vicious from Cowboy Bebop. Due to the episodic nature of the show, he's only in 5 episodes, but he's not only the central threat of those episodes, he also plays a huge role in Spike's past.
In NORA: The Last Chronicle of Devildom, Kneel is orginally the Big Bad until Fall shows up, offically taking the role soon after Knell becomes The Starscream. With Knell driving Nora to achieve his full strength by becoming a "true" Cerberus and destroying everything, he can be considered the Bigger Bad.
That is, until the final chapter, where Knell shows up stronger than ever, nearly goes Omnicidal Maniac on all of creation, and officially replaces Fall as the Big Bad until he is consumed by the Cereberus Vortex.
The same is true for D.Gray-Man's Millennium Earl. Though in later chapters, The Fourteenth and Apocryphos have been challenging him for the position, making it more of a Big Bad Ensemble.
Daimos: Olban was the real Puppet Master caused the conflict in the story, manipulating everybody to achieve power.
Digimon Tamers first had HYPNOS, then Zhuqiaomon, and after this the D-Reaper. Impmon was originally intended to be this (which is why he's portrayed in typical Big Bad fashion in the early promotional material), but Konaka later changed his mind.
Fushigi Yuugi has the infamous Nakago. In the OVAs, Tenkou takes the throne. He's a demonic king.
Kazuhiro Mitogawa in Ga-Rei, virtually kick-starting the entire series as of Ga-Rei Zero- by giving a Sesshouseki to Mei, and then to Yomi, and is also implied to have been the spirit which killed Kagura's mother.
That said, he's still second to Bigger BadLord Tamamo.
The Claw from GUN×SWORDis a sweet old man, with a track record of crimes agains the protagonists as long as his artificial right arm. Every single bad thing in the series ultimately traces back to him.
InuYasha: Naraku was behind almost everything that happened in the story from generational family curses to destroying an entire clan of youkai-slayers, to destroying tribes of youkai to pissing off technically neutral youkai, destroying the lives of the titular hero and his first love, and even being behind the heroine travelling through time. He's behind most of the major destruction of towns, villages, noble clans and even the destruction of entire sacred mountains. There's almost nothing he hasn't been responsible for... including ensuring the release of the Ultimate Evil and the near-success of the true plan of the Artifact of Doom.
Sekidousai in Inukami!, whose inventions form the basis of early plots and those Evil Plan drives the second half of the show.
Dio Brando in JoJo's Bizarre Adventure. Every arc that doesn't feature him as the main villain features one who is connected to him, however small. The Pillar Men (Part 2) created the Stone Mask that turned Dio into a vampire, Yoshikage Kira (Part 4) got his Stand abilities from one of the arrows that Dio once owned, Diavolo (Part 5) was directly responsible for Dio getting his hands on the arrow in the first place, and Enrico Pucci (Part 6) was Dio's closest confidante.
Kara no Kyoukai has Araya Souren, who is responsible for everything before and after Ryougi Shiki, the main character, woke from her coma. Strangely enough, he is finished off in the fifth movie in a series of seven movies.
Kenichi: The Mightiest Disciple presents us with Saiga Furinji, the eponymous One Shadow in the Yami organization's One Shadow Nine Fists group—essentially, the strongest martial artist in the organization—who is also the son of the series' Big Good, Hayato Furinji, and the Disappeared Dad to Hayato's granddaughter Miu. However, it seems Saiga may be a complicated case of this, as he's been shown to still be a Martial Pacifist despite being the leader of a group that advocates murderous martial arts.
Kill la Kill: At first, you're led to believe Knight Templar Satsuki Kiryuin is this. Subverted, when it turns out she's actually been preparing Ryuko to help her defeat the true Big Bads — Evil Matriarch Ragyo Kiryuin and the primordial Life Fiber. Satsuki is actually the Big Good, just one willing to be utterly ruthless in her quest to save humanity.
Kinnikuman has had, in terms of Big Bads that were actually dangerous, Robin Mask for the 20th Choujin Olympics arc, Warsman for the 21st Choujin Olympics arc, Buffaloman for the Devil Choujin arc, Akuma Shogun for the Golden Mask arc, the tag-team of Neptuneman and Big the Budo for the Golden Mask arc, and lastly Kinnikuman Super Phoenix for the Throne arc.
Kotetsu Jeeg: Queen Himika for the first half, Emperor Dragon for the second.
A rare work where the "villain behind everything" isn't even a character is Lupin III: Dead or Alive. The Nanomachines are the ultimate source of conflict, providing an initial challenge, and defeating the Protagonists several times early on. The main plot for Lupin's gang is to discover the secrets of Drifting Island, which is protected by the nanomachines. Even General Headhunter is subordinate to the nanomachines, because he is a robot constructed by them.
Mahou Sensei Negima! has Fate Averruncus, who may or may not be the biggest threat. Although it's later revealed that Dynamis is actually running CE and he actually brought Fate back for additional muscle, making him the Big Bad and Fate merely The Dragon.
In the past, the Lifemaker was undeniably the Big Bad. And may still be the Big Bad.
In MÄR, it's the Caldean Orb, the swirling mass of all of Earth's evil energy that formed a consciousness. It's pretty much behind the entire plot, manipulating everyone.
Naruto initially presents Orochimaru as the Big Bad. The series becomes a Big Bad Ensemble in Part II, featuring Orochimaru, Pain, Danzo, Kabuto, Madara Uchiha, and Tobi as contenders for the title. However, the series appears to have settled on a Big Bad Duumvirate with Tobi, aka Obito Uchiha, the true leader of Akatsuki and the one who instigated the events of the series and the resurrected Madara Uchiha, his Predecessor Villain who came up with the Evil Plan and left it for Tobi to carry out after he died. Later on, Obito makes a Heel-Face Turn and Madara, after being fully revived and becoming the next Sage of the Six Paths, is (literally) backstabbed by Black Zetsu, who reveals that he is not the manifestation of Madara's will, but Princess Kaguya's will. The next chapter has Madara forced to absorb Black Zetsu and a ton of chakra, transforming him into Kaguya herself, cementing her place as the true final villain of the series. This borders on the Ass Pull line as it came about with little to no foreshadowing, and Kaguya herself wasn't even introduced until the last arc, forty chapters ago.
Pokemon 3: The Unown. Molly Hale's actions are driven solely from the desire to be reunited with her missing parents, and they're the ones who granted her the power to do it. Plus, her father was trapped inside of their dimension to begin with.
The All Star movies have Fusion in DX, Bottom in DX2, Black Hole in DX3, Fusion again in New Stage, and Kage in New Stage 2.
The closest thing Puella Magi Madoka Magica has to a main villain is adorable but duplicitous and secretive little Weasel Mascot Kyubey, who doesn't tell the Magical Girls he creates certain key facts, including that Magical Girls are essentially liches, or that every Witch that the Magical Girls fight (aside from those born from familiars) was once a Magical Girl herself — and that they're ultimately doomed to become Witches themselves. Not only that, but he doesn't care one whit about humans as long as the universe itself continues to exist.
If you count Walpurgis Night as a character and not a force of nature then it becomes a Big Bad Ensemble, given its influence on the plot.
Ranma ˝ has Pantyhose Taro, Herb, and Saffron (manga only).
The first season of Rosario + Vampire had Hokuto Kaneshiro. The second season has Gyokuro Shuzen. Later chapters reveal, however, that the realBig Bad is a mysterious figure known as the Masked King, who is the real leader of Gyokuro's organization Fairy Tale. The revelation that Hokuto's organization Anti-Thesis is a "student branch" of Fairy Tale means that the Masked King is the Bigger Bad for the first season as well. A further reveal is that the Masked King is Miyabi Fujisaki, who is in actuality Alucard.
Shishio was the Big Bad of the Kyoto arc by virtue of being Kenshin's replacement as the Ishin Shishi's top assassin, a Social Darwinist whose views clashed with Kenshin's pacifistic ideals, and his desire to overthrow the Japanese government that both his and Kenshin's swords helped to set up. He had the strength, connections, manpower and weaponry to start and maintain his campaign, plus being a magnificentlyManipulative Bastard for a lot of people, both within his private army and on a wider scale; plus his aptitude for planning and executing strategies to keep himself two steps ahead of his enemies. What made him especially effective was that he was willing to cop to his faults whenever any aspect of his planning did fail such as underestimating Sanosuke and not anticipating he'd have portable bombs powerful enough to destroy the Rengoku battleship, he actually respected his underlings to a degree, and he proved powerful enough to stave off four of the strongest opponents he could have—while being physically impaired himself (his burns from the government's assassination attempt meant he couldn't fight longer than 15 minutes at a time or else he'd risk death by overheating).
By contrast, Enishi, the Big Bad of the Jinchu arc, has a much closer tie to Kenshin than Shishio did (both Kenshin and Enishi had Tomoe in common, and both got lasting marks from her death — Kenshin got the second half of his scar, with the first half coming from Tomoe's slain fiance; Enishi, meanwhile, had his hair turn white from the shock of seeing Tomoe die in front of him), being the only one to both physically defeat Kenshin in combat and psychologically break him.
Sailor Moon was no stranger to this concept, but it was even more fond of setting up the season's Dragon as the Big Bad, only to do a big reveal at the end.
First season: Queen Metaria
Sailor Moon R: Ail and En in Part One, and Wiseman/Death Phantom in Part Two
Sailor Moon S: Pharaoh 90
Sailor Moon SuperS: Queen Nehellenia
Sailor Stars: Chaos (who is the original source of all the aforementioned except Ail and En)
Codename: Sailor V, the manga that began before Sailor Moon but that ended after it has Danburite as its Big Bad. Though in the scheme of things he's a small fry, being an underling of the leader of the very first Quirky Miniboss Squad.
The Pope, a.k.a. Gemini Saga, in the Sanctuary Arc of Saint Seiya , Hilda in the Asgard Arc, and the respective titular villains of the Poseidon and Hades Arcs. The movies have their own Big Bads as well.
In the final arc of Shakugan no Shanamain character Yuji becomes the Big Bad after ascending to Snake of the Festival. Howeverm the Snake of the Festival and Yuji succeed in creating a new world for Crimson Denizens to live without having to consume humans' Power of Existence. The Crimson Lords' and Flame Haze's fear that this would destroy the world is resolved by the Denizens deciding to compromise with the Flame Haze despite having won, and the eternal war between the Denizens and Flame Haze end. The Flame Haze are now free to be actual people instead of walking weapons whose only purpose is fighting, something Yuji desperately wanted for Shana, who he does end up in a relationship with. Everything went exactly according to the Snake and Yuji's plans.
Slayers NEXT: Chaos Dragon Gaav and Hellmaster Phibrizo.
Slayers TRY: Valgaav and Dark Star Dugradigdu
Slayers Revolution: Zanaffar (revived by Dulcis)
Slayers Evolution-R: The ghost of Rezo-Shabranigdo.
And in the final original light novel, another piece of Shabranigdo, held within the soul of a mercenary named Luke, was a Big Bad.
Sonic X has Dr. Eggman in the first two seasons and Dark Oak in the final season.
Soul Eater has one for every major story arc. In the first one, it's Medusa, the second, Arachnae, and the third, Noah (The Greed Incarnation) but actually it's the Book of Eibon's Table of Contents as the Noahs are artificial constructs created by it.. Although Medusa is notable, in that she wakes up Kishin Ashura and wasn't killed in her arc, continuing to be an active villain until she was killed by Crona at the beginning of the Moon Arc (which was even part of her plan). While Kishin Asura could be interpreted as the Big Bad of the entire series (given that Soul Eater is about preventing Kishins from being born just like Asura, and that everybody is after him), for most of the story he qualifies better as the Bigger Bad. While he did make a few recurring appearances in the story arcs, unlike Medusa and the other major villians most of his influence was indirect. It's only until the Moon Arc that he takes center role as the Big Bad.
Windaria The king of the Shadowland appears to be this but its actually Lagado.
Lord Darcia in Wolf's Rain is not only a Big Bad, his entire family line is responsible for anything evil involved in the story... even in its "happy ending," which is anything but because of him.
Oddly enough, the original ending (the version that stops at episode 26) seems to present Lady Jaguara as the real villain, especially after Darcia's apparent death. In the OVA, Darcia takes that position back hard.
Yu-Gi-Oh!: The manga and second series anime have an overall Big Bad, Dark Bakura (A.K.A. the Spirit of the Millennium Ring), who works on his scheme the whole series. In terms of individual arcs:
First Arc (manga and Season0): Shadi (though he's not evil, he just subscribes to Ancient Egyptian standards of morality).
Death-T (Manga and Season 0): Seto Kaiba.
Monster World (Manga and Season 0): Dark Bakura (The Spirit of the Millenium Ring).
Season 1: Rex Godwin starts off looking like one, but turns out to be more of a Stealth Mentor. In the second half of the season, Rudger (Rex's brother and leader of The Psycho Rangers) seems to take over, but is soon abruptly killed off halfway through his arc, leaving the rest of it to his followers who had been Dragon Their Feet. The final three episodes of the season, however, reveal the guy behind everything: it really was Rex the whole time, playing everyone up to and including two deities for suckers.
Season 2: Z-one, who was, through his followers, responsible for Rex and Rudger turning evil, and thus could be considered the Bigger Bad for Season 1, as well.
Onimaru Takeshi in Yaiba, your typical overlord. Also Kaguya and, during the Pyramid and Underworld arcs, Boss.
Season 2: Appears to have a committee of four villains: Gilag, Misael, Alit, and Durbe, though Durbe is pretty clearly dominant. Vector was also posthumously revealed to have been a member of this group, as well, so a pretty good case could be made for these guys being the Big Bad the whole time. Vector becomes the Big Bad after he is revealed to be still alive and trying to resurrect the Barian leader, Don Thousand.