"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.
The Adventures of Brisco County, Jr.: The main Big Bad is John Bly, who is eventually revealed to be an even bigger threat than previously thought when it is discovered that he's actually a time traveler from Earth's far future who will institute a 1,000-year reign of terror.
Alphas: The main villains are the Red Flag organization, the collective Evil Counterpart to Rosen's Alpha team. Specifically, the Big Bad would be Red Flag's leader, Stanton Parish, who so far has only been on screen for about five minutes total in season 1 finale, but has still managed to show himself as a master Chessmaster, and a very dangerous opponent.
Angel has the Senior Partners at Wolfram and Hart as the main antagonist for the entire series, who were never properly seen and worked through their various lawyers and other agents like Lindsey, Lilah and Hamilton. On occasion their plans are disrupted by other evil forces but they represent the overriding evil Angel has to face.
Season 4 has Jasmine, ostensibly one of The Powers That Be who manipulated events across the series in order to gain a physical form. She had her own Dragon, The Beast, who massacred the LA Wolfram & Hart branch.
Season 5 returned to the Senior Partners, but with a twist in that Angel and his team were given Wolfram and Hart resources to do whatever they wanted with, making it an Enemy Mine situation. They kept their presence known through their Dragons, Marcus Hamilton and the Circle of the Black Thorn led by Archduke Sebassis.
Since Arrow runs two storylines simultaneously (one in the present, the other flashbacks to Oliver's time on the island), it naturally has two Big Bads per season.
Blake's 7: Had Servalan, especially in Season 3 when she's risen to President of the Federation and is answerable to no-one. Despite her reduced status in Season 4, she's still ultimately behind most of the problems the Seven face.
For a while, it looked as though Fring might be a lesser threat than the brutal Mexican drug cartel to which he paid tribute in return for jurisdiction over his meth market. He put those doubts to rest when he successfully assassinated the cartel's leadership.
Subverted twice with Mr. Trick, initially played off as the Big Bad himself, then as The Dragon when the true Big Bad shows. Then the real Dragon shows...
Season 4: Most of the season has no Big Bad, although Spike returns early on as a decoy Big Bad and Professor Walsh is shaping up to be a good candidate before she is killed mid-season. Late in the season, Adam first appears as The Dragon and becomes the Big Bad and Final Boss.
Season 6: Appears to have a Big Bad Triumvirate in the form of The Trio of Warren, Johnathan, and Andrew. It quickly becomes clear that Warren is the dominant personality of the three, and he becomes the Big Bad of the season, with his murder of Tara ultimately causing Willow to snap and become the Final Boss after killing him. Joss Whedon has claimed that "life itself" was the Big Bad of Season 6.
Season 1: To some extent, Rex Buckland and Hannah Webster in the first half of the season.
Season 2: No Big Bads.
Season 3: The Triad & Cole Turner.
Season 4: The Source.
Season 5: No Big Bads.
Season 6: Gideon.
Season 7: Zankou from the demons and Inspector Sheridan in the "real world".
Season 8: The Triad and Christy Jenkins.
Chuck: None present in Season One, but subsequent seasons had them:
Season Two: Ted Roark.
Season Three: Daniel Shaw
Season Four: Alexei Volkoff
Supplanted by his daughter Vivian Volkoff in the second half of the season.
Season Five: Decker
Seeing as he's been blown up, he's been supplanted by Daniel Shaw, the real person behind the conspiracy to bring down Chuck.
With Shaw depowered and imprisoned, he's been supplanted by Nicholas Quinn, who will be the series's final Big Bad.
Ted Roark and many season one villains were part of Fulcrum, which in turn was part of The Ring, which was run by The Director and The Elders in season three, and was responsible for Daniel Shaw's fall to evil.
In the second half of City Homicide Season 2, Billy Pierce fills this role as he frames Superintendant Waverley for corruption, before kidnapping and murdering her teenaged son.
Community did without for two seasons, but as in season 3 Chang steadily rose to power after the previous season's Humiliation Conga, taking over the school in the four-part finale and kicking out the Greendale Seven.
Season 1: Mary Alice Young, since she was the one who killed Deirdre.
Season 2: Matthew Applewhite
Season 3: Gloria Hodge
Season 4: Wayne Davis
Season 5: Dave Williams
Season 6: Patrick Logan
Season 7: Felicia Tilman
In Dexter, the hero is also the villain, in a version of the Villain Protagonist and Heroic Sociopath tropes, so in one sense Dexter is always his own Big Bad. Each season has its own exterior Big Bad as well.
Season 1: The Ice Truck Killer, who is actually Dexter's brother, Brian, who is a doctor working on the case with the police.
Season 2: Dexter is clearly his own big bad, as he's trying to avoid being caught. There are superficial decoy Big Bads: Lundy, the would-be Hero Antagonist, Doakes, and finally Lila.
Season 3: Miguel Prado.
Season 4: Trinity.
Season 5: Jordan Chase.
Season 6: Professor Gellar and Travis Marshall. But it turns out it's just Travis. Gellar was Dead All Along.
Season 7: Isaak Sirko, Hannah McKay, and Maria LaGuerta, although LaGuerta is a Hero Antagonist.
Season 8: The Brain Surgeon (aka Oliver Saxon/Daniel Vogel)
Dollhouse had Alpha causing every problem the Dollhouse crew faced in Season 1. Season 2 has the Rossum Corporation as a whole set up this way, but only as of "Getting Closer" (2x11) do we know who the Magnificent Bastard in charge of it is: Boyd Langton.
Double The Fist has no main antagonist, but Mephisto has entered a similar situation at least twice.
In "Bush Bash", he is possessed by a Demi God and tries to destroy the forest (And the Fist Team) using an army of cloned... lumberjack pandas...
In Series Two, he almost plays the trope straight by secretly joining the Medieval Recreationists as their leader, and formulated a Evil Plan against the team.
Seasons 2 to 4: The Daleks, the main villains of practically every story longer than four episodes. The Meddling Monk serves as Final Boss of Season 2 but is too much of an Ineffectual Sympathetic Villain to really qualify.
Season 5: The Cybermen and the Great Intelligence
Season 8: The Master; he was the villain of literally every episode. Possibly qualifies for Season 9 as well; he appears less but is still regarded as the biggest threat to Earth by UNIT. The Master basically played this role for the Third Doctor's era (although he doesn't appear in Seasons 7 or 11).
Season 10: The Daleks, who act as the True Final Boss above the Master, employing him to start an interplanetary war to destabilise the region while preparing a giant invasion force to take over in the aftermath.
Season 15: The Sontarans, who are indirectly responsible for the events of the season opener before turning out to be behind the Vardans in the finale.
Season 16: The Black Guardian, but he doesn't show up until the final episode.
Seasons 18 and 19: The new form of the Master.
Season 20: The Black Guardian
Season 23: The Valeyard and the Time Lord High Council.
Season 26 reveals that Fenric caused everything in the previous three seasons.
Series 1: The Dalek Emperor and his faction of half-human Daleks.
Series 2: Started off with John Lumic and his version of the Cybermen. They return for the finale, now led by a generic Cyber-Leader, but they're usurped by the Cult of Skaro (led by Dalek Sec); both factions spent more time fighting each other than the heroes.
Series 4: Featured the resurgent Dalek Empire, represented by Davros, but he's technically a "pet" for the Supreme Dalek.
Year of Specials / The End of Time: Rassilon, founder of Time Lord society, brought back during the Time War so he could save his people - even if it means destroying the rest of the universe.
Series 5 / 6: "The Silence", a movement determined to kill the Doctor in order to avert a prophecy that he will reveal his most terrible secret. Indirectly caused most of series 5 despite not appearing until the series 6 opening.
Series 7 has the Great Intelligence. While it doesn't show up until the latter half of the season, its indirect involvement through Clara stretches back to the start of the season.
Anniversary Specials/The Time of the Doctor: The Daleks. The specials have something of a Big Bad Ensemble but the Daleks are the most dangerous and the last ones standing.
Big Finish Doctor Who has a few as well. The villains for the Eighth Doctor's stories before the Divergent Universe Arc are the Neverpeople and Rassilon. The villain for the Divergent Universe arc is again Rassilon.
The Meddling Monk in the New Eighth Doctor Adventures Series 4, though at the end he is eclipsed by the Daleks.
Farscape: A succession of Big Bads. First it's Crais, then Scorpius, then Grayza, who eventually shares the limelight with the Scarran Emperor. Each of these get progressively more epic and ambitious.
It is strongly implied in Firefly that the Big Bad was the Blue Sun Corporation, which apparently worked with the Academy.
Season 6: Ahrimin for the opening arc, Liam O'Rourke for the finale.
Home and Away had the Summer Bay Stalker, AKA Zoe MacCalister, AKA Eve Jacobsen, during 2005 and 2006.
Angie Russell was this in late 2002, early 2003.
Sarah Lewis was responsible for the armed siege that formed the mid-season cliffhanger in 2004.
Suzy Sudiro and Derrick Quaid ran the human trafficking operation that took up the 2009 season.
Criminal gang leader and drug supplier Darryl Braxton seemed to fill this role for the first half of the 2011 season, although the Sorting Algorithm of Evil saw rival gang leader Jake Pirovic move above him for the latter half of the season.
Adam Sharpe filled this role in late 2012/early 2013.
The latter half of 2013 had something of a Big Bad Ensemble between the Sanctuary Lodge cult, led by Murray Granger and Ethan MacGuire, and Sadist Teacher Jade Montgomery, until the two storylines collide in the finale.
Justified: Boyd Crowder tends to be the series' default Big Bad, but each season also has a contender.
Season 1: Bo Crowder and Gio Reyes of the Miami drug cartel.
555 had the Smart Brain heads and the Orphnoch King.
Blade had Hiroshi Tennoji, though at the end of the series he was usurped by Giraffe Undead, the last member of the Royal Club, who was ticked at being used by Tennoji. Ultimately however, the real Big Bad may just have been the Sealing Stone, since it was what created the Undead in the first place.
Decade had Apollo Geist at first, then Eijiro Hikari/Dr. Death and Narutaki/Colonel Zol in the film, who are in turn usurped by the Neo Organism. Again.
Double had Ryubee Sonozaki/the Terror Dopant. He was the first big bad in a while to be revealed as one in the first episode. Most of the heisei Kamen Rider Big Bads are revealed after the halfway point or in the final arc.
OOO had Dr. Maki. Interestingly, he was supposed to just be the big bad for the second arc, and that Ankh was going to be the final villain, but things changed and he became a fully fledged big bad.
Fourze had Gamou Mitsuaki/Sagittarius, who heads Amanogawa High School. It is obvious that he has red eyes whenever he wants to.
Wizard had Wiseman, who is really an alter ego of none other than the White Wizard. Unfortunately for him, Sora/Gremlin steals his weapon and becomes Evolved Gremlin, becoming the final Big Bad of the show.
The Legend Of Dick And Dom: The Beastmaster is a mysterious entity behind many of the protagonists' setbacks in season two (showing up- without his identity being revealwed- at the end of each episode to punish the villains who failed to stop them). He is revealed as the antagonist for season three.
Leverage typically lacks one of these, but in Season 4 we have Victor Dubenich, a former mark out for revenge, who manipulates the events of the season from behind the scenes before stepping into the spotlight in the last two episodes.
LOST had an interesting succession, with the scope of the show panning out to reveal a Bigger Bad.
Season 1: Didn't seem to have a Big Bad originally. The most reoccuring antagonist that season was The Smoke Monster, who seemed more like a rampaging beast, with Ethan being a runner-up, though it's clear he was just a spy and he's killed by Charlie a few episodes before the finale, and it's only in the finale that we see other, well, Others, including Tom Friendly, but they only appear in one scene to kidnap Walt. Though it turns out this season DID have a Big Bad, as the Smoke Monster was the Big Bad of the entire series
Season 2: The survivors originally assume Mr. Friendly is this, but this is confirmed false and instead an unnamed and unseen leader is hinted at. It isn't until the finale when the leader of the Others is revealed to be Benjamin Linus, aka the man who posed as Henry Gale for much of the season.
Season 3: Benjamin Linus. Though hints are thrown at Jacob, the mysterious being the Others worship. Though he is revealed to actually be the Big Good seasons later and never approved of Ben's actions
Season 4: Charles Widmore, though his Psycho for Hire Martin Keamy gets more screentime.
Most of Season 5 skips around with lots of smaller villains, and switching back and forth between Ben and Widmore, until it reveals the true Big Bad of Lost: The Man in Black/The Smoke Monster., who finally plays the primary antagonist role in the sixth and final season directly.
Merlin has had several, but notably King Uther Pendragon, and then Morgana, following Uther's death. However, each season had a back-up Big Bad for Merlin to face when Uther and Morgana were busy, and because of the show's Grey and Grey Morality, it could be surprisingly difficult at times (especially in the early seasons) to pin-point who exactly posed the greatest threat.
Season 1: Nimueh, who is indeed the overall Big Bad of the season, being behind most of the problems in Camelot. Uther is also at his most threatening here, though in later seasons he was more of an Antagonist than an overt villain.
Season 2: The most complex season in terms of villainy. Uther mellowed out a bit and Morgause is initially quite justified in most of her actions and beliefs. Morgana goes through her Face-Heel Turn but is still mostly sympathetic and Kilgharrah's Revenge Before Reason arc is resolved in the finale and never brought up again.note This complexity is the reason why season two is often cited as the best season.
Season 4: Morgana, with Agravaine de Bois as her Dragon who also served as The Mole in Camelot.
Season 5: Morgana, and eventually Mordred. Interestingly, Mordred spends the majority of his appearances not evil, but his prophesied betrayal is the series main arc and biggest threat.
King Odin was also a major threat in the series, until he and Camelot made peace in the final season.
MythQuest: Gorgos is a trickster god who tries to change any myth he's trapped in. He was released by Matt Bellows, and his children Alex and Cleo try to rescue their father while preventing Gorgos from changing mythology.
Charles Durham in the 1985 season, a Villain with Good Publicity who made repeated attempts to obtain an incriminating casette tape from Terri, threatening her and those around her. He was shot dead in a confrontation with Terri in the final week of the season.
In late 2005 and for the first half of 2006, Robert Robinson filled this role, making several attempts on the lives of his father and sister while disguised as his triplet brother.
Nikita had Percy in season 1. For the first half of season 2 he was imprisoned inside Division and replaced as Big Bad by his Dragon, Amanda, but he eventually turned the tables on her and reclaimed the Big Bad mantle. He gets killed at the end of season 2, so Lord knows who it'll be in season 3.
Amanda retakes the Big Bad mantle in season 3, undergoing a campaign of revenge against Nikita and the reformed Division.
Season 1 has a Big Bad Ensemble of Mayor Regina (the Evil Queen) and Mr. Gold (Rumplestilsken). They do work together when it suits their needs, but each has their own agenda and uses the other to further it.
Season 2 is a bit more complex: it starts as a Big Bad Duumvirate between Cora and Hook, before Hook gets booted and Regina becomes Cora's Dragon. Then a new Duumvirate (Greg and Tamara) take over, with Hook working with them for a while. And while all that's going on, Rumplestilsken is still running his own game.
Power Rangers in Space: Dark Specter, who was revealed to be in control of all of the above. Intended to be the final villain, and remains the biggest bad seen on the show to this day. Alternately, Dark Specter is the Bigger Bad while the regular Big Bad position goes to Astronema, the one in charge of the forces that harassed the Space Rangers on a regular basis.
Power Rangers Operation Overdrive: a Big Bad Ensemble with Flurious, Moltor, Kamdor, and the Fearcats; opposed not only to the Rangers but also to one another. Flurious outlives them all and eventually gains the crown and jewels right before the final battle.
Power Rangers Megaforce: Admiral Malkor of the Warstar Armada in the first season, though Vrak got more screentime as the highly competent Dragon-in-Chief. In the second season, Malkor's boss (and Prince Vrak's brother) Prince Vekar shows up with the rest of the Armada.
Season Four follows with Red Coat (aka Cece Drake) as the main antagonist, until the mid-season finale reveals Big A (who commands Red Coat and is actually Ezra).
Prison Break: Vice-President Caroline Reynolds served as the main antagonist for the first and second seasons. Then, she quits her position and is Put on a Bus in order to reveal the true Big Bad: General Krantz.
Season 4, however, has a Big Bad Duumvirate between General Krantz and Christina Scofield.
Revenge: For most of season 1, Conrad and Victoria Grayson, being at the center of the conspiracy to frame David Clarke for their own crimes, hold this position by default. However, by the end of the season it's clear they were ultimately just pawns of the Eviler than ThouAmericon Initiative, who now serve as the Bigger Bad of the series. As of a few episodes into season 2, the Initiative seems to be taking more active steps and moving down into the actual Big Bad role. Then the season finale reveals that the Initiative is just a cover for a group of Corrupt Corporate Executives making money from their acts of terror... and Conrad is now in their inner circle. This definitely puts Conrad right back into the role of Big Bad, pushing out even the horrified Victoria.
The Savage Eye: The British Empire and the Catholic Church, as this is a series about Irish culture and why it is like it is.
Scandal: The first season didn't seem to have one, but Billy Chambers like qualifies. The second season, however, establishes Hollis as this, due to him having 7 people killed and framing someone for it to cover up vote tampering, and having the President himself shot and framing Huck for it! However, it turns out that he didn't have the President shot, Judge Verna did that.
Smallville initially has Lionel Luthor as the main antagonist of Seasons 1-3, although other secondary antagonists, like reporter Roger Nixon, Kal and Jor-El also took a stab at this role in each season respectively. Following Lionel's defeat and subsequent Heel-Face Turn, the situation got a lot more complicated, but played out more or less as follows:
The Season 11 continuation comics have Lex back and causing trouble again on a mostly regular basis, but also have a story arc dealing with the larger threat of theMonitors, who seek to impose order by destroying all life and have already succeeded with Earth-2.
Season 4: The Cartel is a subversion, the real Big Bad is Clay Morrow
Season 5: Damon Pope is set up as this initially, but takes a back seat for much of the season while Clay tries to plot against Jax again before Pope returns to prominence again at the end of the season. So... Big Bad Ensemble?
Season 6: Lee Toric is introduced at the end of season 5 and set up to be the big bad of season 6 until Otto kills him four episodes in. After that it's sort of a toss up between the Irish and Tyne Patterson.
Stargate Atlantis: Although the general premise of the series is the battle against the Wraith, even after four and a half seasons no individual character seems to have emerged as a specific Big Bad. There are currently several prominent candidates, including: Rogue Wraith and Evil Genius Michael; Oberoth (the leader of the Eviler than Thou Replicators); and Affably EvilAnti-Villain Todd, who seems to be making a power play for Supreme Wraith Leader. Had the series continued, it looks as though the Vanyir would have been the next adversary.
Stargate SG-1 has a series of Big Bads, although there are often long stretches in the middle seasons where they becomes fairly uninvolved with the plot.
Silik is almost the Big Bad of the first two seasons, but since he's being controlled by Future-Guy, he fell short. The whole story is never really concluded because the Temporal Cold War doesn't really go anywhere and wasn't very popular.
The Xindi story of season 3 spent most of the time trying to figure out who among the Xindi Council was reasonable and who wanted to blow up Earth no matter what, or the Big Bad. Eventually every Xindi species but the Reptilians started to side with the Enterprise instead of the Sphere-Builders.
Gul Dukat is Deep Space Nine's premier Big Bad. He starts out as a fairly bog-standard antagonist, becomes a sympathetic character (an Anti-Villain if not Anti-Hero), before crossing the Moral Event Horizon and becoming, effectively, the antichrist. He's also the only recurring villain in Star Trek history to kill off a main character.
The Female Changeling serves as the face of the Founders (the leaders of The Dominion), although Weyoun has a fair amount of face time representing The Dominion as well.
For the first two seasons, the ship is hounded by a sect of the Kazon, although the exact Big Bad is debatable: their leader is First Maje Jal Culluh, but The Mole, Seska, has center stage much more often, even going on to menace the heroes a couple more times post-mortem.
A few seasons later, when the Borg take over as Voyager's main adversaries, the role of Big Bad goes to the one controlling them (or the one personifying them, or whatever is going on there), the Borg Queen.
Supernatural's overall Big Bad has actually always been Lucifer, who takes the stage in Season Five. The character who did nearly every action for the entire plan was The Yellow-Eyed Demon aka Azazel, who served as Big Bad in Seasons One and Two. Lilith served the role in Seasons Three and Four.
In Season Six, the position of new Big Bad was up in the air for most of the season, with the best contenders being either Crowley, the new King of Hell, or Raphael, the leader of the angels who want to restart the Apocalypse. Midway through the season, however, Crowley faked his death and we were introduced to an entity known as the "Mother of All", who seemed set to take up the role. But then, Dean killed her, and soon after it was revealed that Crowley was working with Castiel of all people in order to take over Purgatory. So, it looked like they were going to jointly be the Big Bad of the season. But then in the season finale, Castiel tried to cut Crowley out of the deal, so he retaliated by teaming up with Raphael, making it look like they'd be the Big Bads together after all, only for Castiel to Out Gambit them at the last minute, absorb the souls of Purgatory and declare himself the new God. Guess he was the true Big Bad of the season after all.
In the very first episode of Season 7, Castiel gives up his new godlike powers, having realized his mistake — but before he can truly redeem himself, he is replaced by the trueBig Bad — the Leviathans. Thus, for most of the season, our heroes are on the run from a species of monsters who are older than angels with no known weaknesses or vulnerabilities — until Castiel turns out to be alive, heals Sam's mental trauma by taking it onto himself, and recovers enough to help them decode the Word of God, which reveals how to kill the bastards for good.
Season 9 builds on the previous season's Ensemble as it stood at the end of the season: Bartholomew and Malachi emerge as the leaders of the civil war amongst the fallen angels, with Metatron — now in full A God Am I mode — also recruiting in order to secure his own position as sole ruler of Heaven. Meanwhile, Abbadon is continuing to try and usurp Crowley's position, while Crowley himself now a Wild Card.
It's gonna take even longer for Super Sentai than for Power Rangers, but here goes...
Chikyuu Sentai Fiveman: Galactic Empress Meadow. But she was dead the whole time and never evil. The real villain is the ship, Vulgyre, who transforms into Galactic Super Beast Vulgyre.
Choujin Sentai Jetman: Technically didn't have one since the four major villains were competing to see who could kill the Jetmen first for the position, but Count Radiguet is the closest.
Jetman actually subverts this in that the Big Bad is actually Empress Juza, though she just lasts 2 episodes and Radiguet takes over being the show's technical Big Bad (he was formerly the closest for Juza's Dragon)
Tranza also manages to usurp the Big Bad position for several episodes, until Radiguet reclaims that position.
Gosei Sentai Dairanger: Emperor Gorma XV or so it would seem. Turns out he and all the Gorma Tribe higher-ups are actually golems created by Colonel Shadam, apparently The Dragon, who eventually just takes over for real and becomes Emperor Gorma XVI
Hyakujuu Sentai Gaoranger: The Org Master, with the Highness Duke Orgs Shuten, Ura, and Rasetsu being the Dragons in Chief so much that they pretty much count as the Big Bads for an arc each. Unsurprisingly, the Org Master is revealed to be an unsentient figurehead with the Highness Dukes as the actual Big Bads. They soon merge into the final Big Bad: Ultimate Org Senki. For the Milestone Celebration movie, Lost Org Rakushaasa fills the role.
GoGo Sentai Boukenger: High Priest Gaja of the Godom Civilization; Creator King Ryuuwon of the Jaryuu Clan; Gekkou of Illusions of the Dark Shadow ninja clan; and Gai and Rei, the last remaining members of the Ashu Tribe. These four are not only against the Boukenger, but also each other, in the quest for the Precious. Gaja is the final Big Bad, in case you were curious. For this Milestone Celebration movie, Time Demon Chaos is the Big Bad.
Juken Sentai Gekiranger: Rio. Who was manipulated by Long, the Infernal Dragon. Upon learning this, Rio and his Dragon, Mele, perform Heel Face Turns to help fight Long.
Engine Sentai Go-onger: The three Gaiark Ministers, then Kirezky, and finally their boss shows up near the end: Prime Minister Yogoshimacritein.
Tensou Sentai Goseiger: Great King Mons Drake, Makuin of the Blob, and Emperor Robogog the 10th in succession. But in the end it turns out the biggest threat is Bladerun/Buredoran, a.k.a. Brajira of the Messiah, a fallen angel.
Tokumei Sentai Go-Busters: Messiah. He is destroyed in Episode 30, but Enter survived and is acting as the Big Bad while trying to recreate Messiah. Then Escape tries to kill him, succeeds in recreating Messiah, and is reintegrated into him... only for Messiah to die again and Enter to have survived.
Zyuden Sentai Kyoryuger: As of now, Many Faced High Priest Chaos. However, there's a Bigger Bad in the villain that the usual villains are trying to resurrect. And when they succeeded in Episode 22, he was in a mindless state, so Chaos retained Big Bad status as they now try to fix his mind.
Hikonin Sentai Akibaranger: Malshina was set up to be this at first, but behind her there is Dr. Z, the Professor's father, and creator of the Rangers' tech, which was created as a way to cause the simulated monsters and such to leak into reality. Except then the Mind Screw takes over and by the end of the series the trueBig Bad is an Author Avatar of the Toei executive staff.
In season two, season one is canon only in Broad Strokes and Malshina has a Man Behind the Man, General Pain, but he can hardly be arsed to do any real villainy and she has to keep bugging him to make monsters until episode 7. However, it's later revealed that Malshina is the real Big Bad this time and steals the abilities of both General Pain and Saburo Hatte, and the Bigger Bad this time is Prism Ace, an Ultraman Expy.
Reality Show Survivor has at least one contestant with the Big Bad edit every season.
Season 2: Gerard Argent (although the majority of the season has Matt as the Big Bad and the kanima aka Jackson as The Dragon, but then Gerard kills him two episodes before the finale and assumes the role of Final Boss).
Season 3A: Big Bad Ensemble between the Alpha pack leader Deucalion and their sworn-enemy the Darach, later revealed to be Jennifer Blake.
Season 3B: Stiles Stilinski, who was possessed by a nogitsune.
Within the Ultra Series, any opponent that's much stronger than usual typically qualifies as this.
Carl Williams and Mick Gatto.
Underbelly: A Tale of Two Cities: Terry Clark and Bob Trimbole
The Upstairs Downstairs 2010 revival has one, rather unusually for a non-speculative Family Drama: Persie, a Fascist and Nazi spy who wrecks her sister's marriage, nearly destroys her brother-in-law's career, nearly kills Beryl, and otherwise causes most of the trouble on the show. She's more pathetic than menacing, and the chaos she leaves in her wake is haphazard rather than planned, but she's a thoroughly destructive presence.
The Vampire Diaries has Klaus either as a Big Bad or The Heavy. Although most of the enemies they faced were his enemies too, they just had ideas of how to go about opposing him that were incompatible with the interests of the main cast.
Season one has the Founders Council, led by mayor Richard Lockwood. Although the more direct threat is John Gilbert, who acts as the Dragon-in-Chief and The Heavy to both the Fouders Council and Kathrine, respectivly.
Season two starts with Katherine Pierce, but halfway through the season Klaus offically steps up to the Big Bad title.
Season three has Klaus's mother Esther and Alaric, who developed a psycho alter ego.
Season four has Silas, who ownedKlaus of all people.
Season 2: H.G. Wells, of all people, who spends the whole season trying to convince the Warehouse agents otherwise, before stabbing them in the back in order to use an Artifact WMD to begin a new ice age.
Season 3: Walter Sykes, who wants to kill the Regents and destroy the Warehouse as revenge for the Regents stealing an Artifact from him that let him walk.
Xena: Warrior Princess had Ares, Callisto, Caesar, Alti, Dahak and the Olympian gods. Xena may not follow the Seasonal Big Bad formula, but the major villains in the series are all recurring, and (with the exception of Ares and Alti) all follow some form of a linear character arc.
The X-Files generally had a large amorphous government conspiracy as the Big Bad, and the ambiguously described hostile alien race planning to colonize Earth. The former was largely represented by the Syndicate (its most notable member being the Smoking Man), and the latter by the shapeshifting bounty hunter (seasons 2-8) and by the metallic super soldiers (season 9).