"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.
Avenger Penguins - Caractacus P. Doom. As if life could hold anything else in store for a chap with a name like that.
The Avengers: Earth's Mightiest Heroes had Loki as the ultimate Big Bad of its first season, and Baron Strucker, Baron Zemo, the Leader, Kang the Conqueror, and Ultron as Big Bads of smaller arcs within the season.
In the second season, the Skrulls, lead by Queen Veranke, were the main villains for the first half (the second half, being more episodic, didn't really have one, though it was all leading up to a showdown with Galactus).
Vilgax, from Ben 10, is a textbook example. He's wounded grievously in the pilot, drives the plot of most of season 1 from behind the scenes, and finally shows up in person in the season 1 finale, bigger, meaner, smarter, and tougher than anything Ben's faced before. From there on out, he's usually put somewhere between appearances that keeps him from getting involved... He's also an Implacable Man and a Determinator, so he HAS to be kept out of the picture for other plot arcs to happen. Here are the other Big Bads for the following seasons:
Vlad Masters/Plasmius. He's introduced in episode seven, but his influence is felt as early as the opening scenes. Until his Villainous Breakdown, only two people could claim to lay an effective hand on him: Pariah Dark and Jack Fenton, the latter aided with anti-ghost technology. Some have compared him to Slade in deviousness.
Pariah Dark himself, despite only appearing twice, one of those being a cameo during a Gondor Calls for Aid situation, probably counts as well. He's essentially Ghost Darkseid, and is one of the strongest characters, if not the strongest seen in the series.
Each of the double-length movie episodes has one. First is Pariah, as mentioned above. Next is Dark Danny, who is somewhat less powerful but a more personal (and psychotic) threat. Then is the ordinary MuggleFreakshow, who spends the movie trying to get his hands on an Artifact of Doom that will give him reality warping powers. The final Big Bad is not a person, but rather the ecto-asteroid. As Vlad is still the series-spanning Big Bad, he was active in all of these storylines as well (except for the third).
Alvin the Treacherous from Dragons: Riders of Berk. Later becomes a Big Bad Ensemble of Alvin, Dagur, and the Screaming Death in Defenders of Berk until Dagur (nearly) kills Alvin in "A View to a Skrill, Part 2" by using the Skrill to electrocute him to death, then it's just Dagur and the Screaming Death.
Dungeons & Dragons cartoon series: The Evil Incarnate summoned by the Box of Balefire, which Venger attempts to welcome, calling it "master", until it accuses him of failure and reduces his (most recent) castle to a lava-filled crater. Then it goes after the main characters.
Bobby: C'mon, Dungeon Master, who is it? Or what is it? Dungeon Master: His name is not for your ears, Barbarian! He is not life as we know it. He has many identities, on many different worlds! But all know him as... Evil! (Dungeon Master teleports himself and the children to the other side of the world) Dungeon Master: The ruler of many universes! But his goal is to rule the entire cosmos with evil.
Arguably, Tiamat was the more commonly-encountered form. Even Venger hauled ass when she showed up.
Kevin plays this role frequently throughout the series as well.
Thanks to the Sorting Algorithm of Evil, the Big Bad of The Fairly Oddparents has changed a few times. In the first three seasons, Mr. Crocker was Timmy's worst enemy, appearing as the bad guy in every special that had a true villain. "The Big Superhero Wish" was the first special where he was not the main bad guy, and "Channel Chasers" reduced him to a cameo. After that, Anti-Cosmo of the anti-fairies and HP of the pixies took over for the next three seasons as a Big Bad Duumvirate, especially in season six, where the characters never appear separate. Then The Darkness for the "Wishology" trilogy. With the birth of Foop, he took over for season seven (appearing as the villain in that season's finale). The movies are a good example of this.
Channel Chasers: Vicky
School's Out! The Musical: HP and the Pixies
Fairy Idol: Norm the Genie
Fairly Oddbaby: Anti-Fairies and Pixies
Wishology: The Darkness and the Destructinator
There's also the Jimmy/Timmy Power Hour crossovers:
Part 1: Crocker and a malfunctioning Goddard
Part 2: Professor Calamitous and Anti-Cosmo
Part 3: The Villain Whose Name Isn't Shirley
Stewie Griffin from Family Guy was the Big Bad in the early seasons, although this role has been occupied by Carter Pewterschmidt in later seasons.
The Beast With A Billion Backs: Act 1: Dr. Ogden Wernstrom. Act 2: Zapp Brannigan. Act 3: Yivo. Act 4: Bender.
Bender's Game: Mom/Momon.
Into The Wild Green Yonder: The Dark One/ The desert muck leech.
There are two main villains whose overarching schemes drive the plot of Gargoyles: Xanatos and Demona. As the show progresses, however, Xanatos gets character development leading to a Heel-Face Turn (kind of), leaving Demona the unchallenged Big Bad by the time of the Grand Finale. In season 3Castaway and his Quarrymen took on the role, while the (canon) comic continuation has Thailog stepping in to fill the empty shoes of main bad guy.
Depends more on how you look at it: Are they stupid? Yes. But, all Irkens are very materialistic and wasteful, and they are willing to kill everyone on a planet just to they can use them as silly things like parking garages and package shipping.
Depending on whose side you're on, Zim, Dib, or Tak can also qualify.
Looking at it from Dib's POV as the Hero Antagonist, you could say that Zim is the Big Bad trying to take over the world, Tak is the Big Bad's more competent rival, and the Tallest are the Bigger Bad trying to take over the whole universe.
The Big Bad of the Cadmus Arc of Justice League Unlimited was constantly being teased. At first it seemed Amanda Waller was the mastermind, then Lex Luthor, until it was finally revealed in the next-to-last episode as Brainiac, who enters into a Big Bad Duumvirate with Luthor.
Superman: The Animated Series featured an ongoing arc of Superman's struggle with the Galactic ConquerorDarkseid, and his increasingly daring designs on Earth. (By contrast, Lex Luthor's schemes were almost purely episodic in nature.) Darkseid only first appeared in the second season, however: in the first, Braniac was the overarching Big Bad.
Even Ra's al Ghul in Batman: The Animated Series arguably qualified, being introduced in the final moments of one episode, and following up on it later with a cataclysmic two-parter.
There were several contenders for the title in the final season of JLU. At first it looked like Grodd, until he was deposed by Lex Luthor leading to an apparent Big Bad Duumvirate between Lex and the remnants of Brainiac's consciousness. In the end, though, the real threat turned out to be Darkseid. Again.
Dr. Drakken and Shego from Kim Possible are the primary antagonists and the ones that get closest to their goals.
Monkey Fist served as the Big Bad of the Yamanouchi arc, but was treated like a Monster of the Week in the overall series.
The Legend of Korra, set seventy years after Airbender, shifts this role to Amon, Rebel Leader of an anti-bending faction known as Equalists in Season 1. However, it ended up being more complicated than that seeing as Tarrlok, who at first appeared to be the nominal Big Good, wasn't really the nicest guy himself. It turned out that he was another Big Bad all along, as he ultimately betrays everyone by staging a False Flag Operation that would lead him to arrest innocent non-benders before turning on the Avatar and her comrades. Eventually, he was put in his place by Amon. Then it turned out the two of them were brothers, and had been raised by a villain Aang fought and de-powered during the timeskip. Basically, bad parents are responsible for nearly everything in this universe.
Book 2 has Korra's uncle Unalaq, who is the leader of the Northern Water Tribe that is at war with the Southern Water Tribe led by Korra's father Tonraq. However, the real threat is revealed to be Vaatu, the spirit of darkness and the Avatar's ancient enemy, who Unalaq merges with in the season finale to become the Dark Avatar. There's also a Big Bad Ensemble with Varrick.
Legion Of Superheroes had a Five-Bad Band led by The Emerald Empress as the most common villain in the first season, in the second season the Big Bad was definately Imperiex, even though Imperiex was upstaged by Braniac 1.0.
ReBoot has Megabyte. He is the main villain in this show and never suffered from Villain Decay. He even strands Bob in the Web for 10 episodes. Even after the Daemon arc, which threatened the entire net, Megabyte's return invokes a lot more fear in the heroes. This fear is well founded, as Megabyte takes over the Principal office in less than 2 episodes since returning.
Scooby-Doo! Mystery Incorporated: The end of season 1 revealed that Mayor Jones was the one behind the whole plot, and he actively confronted the gang in the finale. However, it could also be argued that he shared the role with ProfessorPericles who is much more active a villain throughout the season. And in any case, at the end of the season the Mayor is arrested, leaving Pericles to take on the role fully.
In the second season, Pericles has formed a Big Bad Duumvirate with Mr. E / Ricky Owens, and clearly holds the more dominant position of the two. Basically, Pericles has secured his place as the Big Bad of this show.
Sheila Broflovski is the co-Big Bad in the same movie, with Satan.
Cartman himself is this, more specifically in the recent seasons and the trilogy "Coon & Friends".
While the The Spectacular Spider-Man had several characters vying for the title of boss of the New York underworld, the title belongs to Tombstone, who serves as the Big Bad for the series until he is deposed by Green Goblin.
In Spider-Man: The Animated Series, the Kingpin and Norman Osborn/Green Goblin took turns vying for this title, though much moreso the Kingpin than Osborn.
In the 2003 cartoon, he cements his position as the Big Bad even further by making plenty of Xanatos Gambits.
The Tengu (the demon whose legend inspired the Shredder) for season four and five and DariusDun in season six. The 'original' Shredder made his triumphant return in season seven as a digital program and in the flesh in the concluding film.
The 2012 cartoon currently features a Big Bad Ensemble between the Shredder and Kraang Prime.
There were, however, four Bigger Bads behind Mumm-Ra, who are never confronted directly and only appear in statue form. Mumm-Ra isn't even their strongest follower; that honor goes to Pyron, who appeared out of nowhere to be the Final Boss of the original series.
In each season of Total Drama, there's a contestant that's causing the most trouble.
Island: Heather, and the most iconic one at that, her role is also sometimes backed up by Duncan, depending on weather or not he's nice.
Pahkitew Island: Scarlett, but she's eliminated in the very episode where she fully takes over, along with Max, which means Dave takes over this position in the finale.
Ezekiel also serves as the antagonist for "I See London" in World Tour, and "Zeke and Ye Shall Find" in All Stars (the 100th episode of the series), where, in both of these respective episodes, he kidnaps contestants in a horror-themed challenge.
Megatron in almost every incarnation of Transformers, only to usually force an Enemy Mine when Unicron appears.
Generation 1: Led the Decepticons on Cybertron and constantly tried all sorts of evil schemes to steal energy from Earth. Since these plans tended to fail, the writers eventually resorted to an Enemy Mine plot every other episode to avoid Villain Decay.
In Beast Wars, he was the Big Bad twice. Firstly he's the standard ruler of the Predacons, fighting against the Maximals. During The Reveal, it is shown that the G1 Megatron had orchestrated the plan, ordering the Beast Megatron to go back in time and kill the G1 Autobots while they were in stasis. Only for that plan to be ignored. Beast Wars Megatron only followed this plan as a last ditch effort, in only one plot, which failed. (Thankfully so, or they all would have been killed by Unicron at some point). Other plots include successfully killing both Optimuses (Optimi?), inventing new classes of Transformers (Transmetal 2, Vehicons) and introducing ham to prehistoric Earth.
Beast Machines: succeeds in conquering Cybertron and ruling over a planet of mindless, sparkless drones. All this happens before the series begins. During the series, he absorbs every spark on the planet and comes within a millimetre of godhood. Yes, godhood.
Armada: Leads the Decepticons and gets his servos on the three most powerful minicons in the universe and would probably have destroyed the Autobots if Unicron hadn't forced them into an alliance.
Energon: Rallies the Decepticons into once again fighting against the Autobots, then hijacks Alpha Q's plan to restore his home planet and instead manages to successfully revive and, for a time, control Unicron. Oh, and he reformats Scorponok's and Demolishor's sparks to make them less moral and more loyal to himself.
Cybertron: Goes after the Omega Lock and the four Cyber Planet Keys to steal the power of Primus and become a god. He intends to use the Unicron Singularity to destroy the universe and then recreate it as he pleases. Starscream successfully betrays him and nearly usurps this spot, but Galvatron beats him in an epic showdown. Luckily for the universe, he is beaten on the verge of success and is slain by Optimus Prime in another epic battle.
Transformers Animated: His body was destroyed in the pilot, leaving him a head in a scientist's lab. Hooked into the lab's computers, and with the right words to Professor Sumdac, he spends the first season working on getting a new body and taking shots at the Autobots through intermediaries. When he gains a new body and comes bursting out of Sumdac Tower in the first season finale, the 'bots know exactly how screwed they are. Circumstances still force him to spend most of his time plotting, but it's still a step up from "Decepticons, RETREAT!"
Transformers Prime: Arrives on Earth via space bridge during the Five-Episode Pilot, armed with "Dark Energon", which has the power to revive Cybertronian corpses as mindless berserkers. The mini-series ends with him and an undead army disappearing in a space bridge explosion. Starscream promptly becomes the Dragon Ascendant and takes over as Big Bad for the next several episodes, but Megatron is ultimately revived and retakes the top spot. In the last few episodes of Season 1, though, he's overshadowed by Unicron as the premier threat, only to retake the position in Season 2. . This series so far as a pattern of alternating between Megatron and someone else for chunks of episodes, going Megatron-> Starscream-> Megatron-> Unicron-> Megatron.
Unicron will be the Big Bad of "Predacons Rising".
The Japanese series have added some other Big Bads, such as Scorponok, Devil Z, Overlord, Deathsaurus, Violen Jiger, and Dark Nova.
The Japanese sequels to Beast Wars also had their own. Beast Wars II had brothers Galvatron and Megastorm, and Beast Wars Neo had Magmatron.
The comics also added a few of their own, including Shockwave, Thunderwing, Ratbat, Bludgeon, Soundwave, Straxus, Scrash, Trannis, Clench, and Jhiaxus. The finale of the Generation II comic revealed that ALL of the G1-era Big Bads were unknowingly reporting to Liege Maximo, the very first Decepticon. Unfortunately, the comic was canceled immediately after this revelation, so that storyline never went anywhere.
X-Men has Apocalypse in a more series-wide capacity, since Magneto's Heel-Face Revolving Door was played up. Mister Sinister clearly holds this status in Season 2, though.
In X-Men: Evolution, Magneto is the Big Bad for the first two seasons, and Apocalypse takes the role in the last two.
And in Wolverine and the X-Men, Mastermold is the Big Bad of the Bad Future Xavier is stuck in, while Magneto and Senator Robert Kelly largely takes the role among several long-term villains Though the Inner Circle also has a pretty good claim on driving a lot of the plot. The Sequel Hook set up Apocalypse as the Big Bad for an aborted second season.
In Season 2, the Light shares the role of Big Bad with their mysterious "partner", later revealed to be the Reach, who are led by the Ambassador, the Scientist, and Black Beetle. Of course, both groups are also using and plotting against the other and at the end of the season, Black Beetle takes full command of the Reach and sets in motion the doomsday threat the heroes must deal with in the Grand Finale.
However, the very last scene of the final episode revealed that the Light (or at least Vandal Savage) had been working with Darkseid the entire time, implying that the Lord of Apokolips would have stepped up to fill this role had the series continued.