&"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.
Season 7: Alan Wilson, although Jonas Hodges got more screen time.
Alan Wilson and Jonas Hodges were both in the same Omniscient Council Of Vagueness behind the season's events, Wilson was "first among equals" so to speak.
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 the first season finale, but has still managed to show himself as a master Chessmaster, and a very dangerous opponent.
Angel has Wolfram and Hart as the main antagonist for the entire series, though they were not always the Big Bad.
Season One has Wolfram and Hart.
Season Two begins with Wolfram and Hart, though they are upstaged by Darla and Drusilla halfway through the season.
Season 2: First the Anointed One was a decoy big bad. Spike and Drusilla are the Big Bads of the first half of the season, and Angelus is the big bad of the second half after his Face Heel Turn.
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 . Late in the season, Adam first appears and becomes the big bad.
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 8 Comic: Twilight, the sentient dimension, not Angel.
Season 9 Comic: Apparently rogue Slayer Simone Doffler... though its too early to tell.
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.
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: To some extent, the Crone.
Season 6: Gideon.
Season 7: Zankou from the demons and Inspector Sheridan in the "real world".
Season 8: The Triad and Christy Jenkins.
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.
Season 1 and 2: Evil Genius serial killer Paul Millander
Season 5: Arguably the team's Smug Snake superior Conrad Ecklie. He never does anything illegal, but most of the season's non-crime conflicts (the team breaking up, Sophia being demoted, Catherine turning against the others) trace back to him.
Season 7: The Miniature Killer aka Natalie Davis
Season 7 Keppler mini-arc: Corrupt Cop Frank McCarty
Season 8: Crime boss Lou Gedda, usurped by Undersheriff McKeen
Season 10: "Dr. Jekyll" aka Charlie Dimasa
Season 11: Nate Haskell, after serving as a secondary villain in several earlier season episodes.
Season 12: Laura Gabriel for Catherine's departure arc and McKeen again in the finale
Likewise, CSI: NY had Shane Casey, the 333 caller, the Cabbie Killer, and the Compass Killer.
Chuck: None present in Season One, but sub-sequent 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.
"Community:
Season 1: Senor Chang, who's difficult class brought the study group together.
Season 2: Pierce who's standing deterioated with the group after Advanced Dungeon & Dragons.
and City College, Greendale's rival.
Season 3: Uncertain. But it's a tie between Chang, who's security force is beginning to make it's bid for the school, and Vice Dean Laybourne who wants Troy to join the Air Conditioning Annex and end their friendship with Abed.
Season 1: Manticore, at first personified by Colonel Donald Lydecker, who was later ousted by the Eviler than Thou Madame X.
Season 2: Ames White, who is secretly a government agent assigned to cover up Manticore by hunting down transgenics, and even more secretly a leader in the Familiar Breeding Cult.
Season 1 of Dark Oracle has Evil SorcererOmen, who is revealed to be the one who saddled Lance and Cally with the Dark World comic in the first place. In Season 2, Vern makes a valiant attempt at becoming the new main villain, before being upstaged by Omen's return. Omen himself has Blaze and Violet in back of him, while The Puppet-Master is in back of them.
Desperate Housewives has a major mystery for each season, thus who committed said crime can be considered as the Big Bad.
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
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.
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 - oh, and they're still around at the end of that series, so we can probably expect them in 7.
The original Doctor Who series had more of a Monster of the Week format but had the Master as the Big Bad in Season Eight and the Black Guardian in Season Sixteen. They were also the Big Bads of mini-arcs in Seasons Eighteen/Nineteen and Twenty respectively. At first glance the Valeyard seems to be the Big Bad of Season Twenty-Three but in reality he's more of a Dragon with an Agenda or Starscream and the real Big Bad is the corrupt Time Lord High Council
Farscape: A succession of Big Bads. First it's Crais, then Scorpius, then Grayza, who eventually shares the limelight with the Scarran Emperor. Note that 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.
Volume 4: Initially Nathan, then usurped by The Dragon Danko, who is in turn usurped by Sylar in the season finale.
Volume 5: Samuel Sullivan
Home and Away had the Summer Bay Stalker, AKA Zoe Mac Calister, AKA Eve Jacobsen, during 2005 and 2006.
Angie Russell was this in late 2002, early 2003.
Suzy Sudiro and Derrick Quaid ran the human trafficking operation that took up the 2009 season. Arguably Hugo Austin, although his motives are ambiguous.
Justified has Bo Crowder and the Miami drug cartel in Season 1, and then Mags Bennett in Season 2. Wynn Duffy, head of the Dixie Mafia, may be getting set up to play this role later on, as might Boyd Crowder.
Black RX had Grand Lord Crisis, who... may be Great Leader, it's not entirely clear, but they have the same voice actor, whose distinctive voice was Great Leader's calling card.
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.
Hibiki had The Man and The Woman and all their myriad clones. We don't even meet the actual originals until the finale. And its even possible that they aren't the originals after all...
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.
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.
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.
In late 2005 and for the first half of 2006, Robert Robinson filled this role on Neighbours
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.
Power Rangers Mystic Force: The Master was the big one, but there was a series of villains under him that took command in his stead: Morticon, Imperious, and Sculpin.
Power Rangers Operation Overdrive: Flurious, Moltor, Kamdor, and the Fearcats; opposed not only to the Rangers but also to one another.
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 that the Big Bad is actually Empress Juza, though she just lasts 2 episodes and Radiguet pretty much 'takes over' for 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.
Kyoryu Sentai Zyuranger: Contrary to popular belief that Bandora is the Big Bad, Dai-Satan holds the position seeing as Bandora is his minion. However, seeing that Satan NEEDS to be summoned by Bandora and is never supervising the day-by-day villainy or reprimanding Bandora for her mistakes, Bandora can still count as the 'technical' Big Bad.
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
Denji Sentai Megaranger: Arguably Dr. Hinelar. While he does have a superior, Electric King Javious, the latter is a major The Man Behind the Curtain, and Hinelar knows this and ends up usurping him
Mirai Sentai Timeranger: At first seems to be Don Dolnero, later revealed to actually be Gien and Captain Ryuya.
Hyakujuu Sentai Gaoranger: Actually had THREE Big Bads that merged into one and kicked the heroes around, even kill the source of their powers. Of course they got better.
Tokusou Sentai Dekaranger: None. All the villains are independent. The closest would be the sole recurring baddie Agent Abrella, who sells them their weapons. Though he does seem to take that role well when he executes the All Your Base Are Belong to Us plan.
Go Go 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.
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, a.k.a. Brajira of the Messiah, a fallen angel.
Season 2: Armadillo for the first half of the season or so.
Season 3: The Armenian mob and Margos
Season 4: Antwon Mitchell
Season 5: This season plays around with this a bit with Jon Kavanaugh who is more of an Anti-Villain until his desire to take down Vic drives him to become a Fallen Hero.
Season 6: There isn't really one this season but it does set up some Big Bads in waiting in the form of Pezuela, the Armenians and Shane.
Season 7: Has a Big Bad Ensemble with Pezuela, the Cartel, the Armenians, Lloyd and Shane.
Sliders after its premise was changed:
Seasons 1 & 2: Original premise, no Big Bads.
Season 3: Colonel Angus Rickman.
Season 4: The Kromaggs.
Season 5: Doctor Oberon Geiger.
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:
Season 6: Lex Luthor. Yeah the zoners are out there, and Bizzarro's waiting in the wings, but Lex is The Heavy for the season, and is behind almost every problem in series.
Arguably, WARLORD SHANK (that's the only way to pronounce his name) is the Big Bad of Space Cases, as he made the most appearances of any villain and was in both Season Finales.
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 evil Asgard 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 takes 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. So I guess he was the true Big Bad of the season after all.
In the very first episode of Season Seven, 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 an entire 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.
Underbelly: Arguably Carl Williams and Mick Gatto.
Underbelly: A Tale of Two Cities: Terry Clark and Bob Trimbole
The Vampire Diaries has Klaus. 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 1: James McPhearson, who wants to steal Artifacts and sell them to the highest bidder, and also invoke a Start of Darkness in his former friend Artie.
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.
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).