Marceline's dad, Hunson Abadeer, is the Satan equivalent of the Adventure Time universe, but not a major force in the plot. However, he only counts in the early seasons in which the Ice King is the Big Bad; later seasons introduce villains even more evil and more of a greater scope than him.
Gunter is implied to be the most powerful evil force in Ooo, even surpassing Marceline's Dad and the Lich. As of "Orgalorg", this has been confirmed; Gunter is in fact an evil god named Orgalorg who predates the universe and can destroy planets on a whim when at full power. The only thing preventing him from being a major force is that being sealed in a penguin erased his memories.
As of Season 8, we have solid evidence that GOLB, a mysterious, sinister entity who has appeared in only a couple episodes, may in fact be this to the entire series: his attack on Mars in the past is a central part of Magic Man and Grob Gob Glob Grod's backstories (including rendering Magic Man's wife Deader Than Dead, to the point that even Prismo can't bring her back); he is hinted to be as powerful, if not more so, than Grob Gob Glob Grod; and perhaps most significantly, the Lich himself- previously the closest thing the show had to a singular Big Bad- describes himself as "the last scholar of GOLB". He then appears in the Grand Finale, thus becoming the Final Boss.
The lovecraftian monsters before the dawn of creation (according to the Lich) may even be this to GOLB, Orgalorg, the Catalyst Comets, and any other monstrosities that transcend reality, all of which may even have been who the Lich was speaking of.
The Lich: "Before there was time...before there was anything, there was nothing...and before there was nothing...there were monsters."
American Dragon: Jake Long: While the Huntsclan is still Jake's primary enemy, they're ranked as only the number 4 threat to the Magical Community. Instead, the Dark Dragon serves as the most powerful enemy in the series, and thus only gets personally involved in three episodes.
Angel's Friends: Cassidy and Kubral, the two warlords that started the war between Angels and Devils, and the ones who are indirectly responsible for Reina turning evil, Angelie's disappearance, and the events that Raf and Sulfus have faced.
Avatar: The Last Airbender: Ozai served this role is seasons 1 and 2 as he never has any direct contact with the heroes, not even Zuko save for a flashback, and only becomes directly involved in season 3, where his face is actually shown.
Season 2 reveals Vaatu to be the canonical ultimate evil of the entire Avatar universe, as he is the embodiment of darkness, chaos and destruction. He was also indirectly the reason the Avatar came into existence. It's not until Korra's time that he steps down to take the Big Bad seat for that season.
The Red Lotus serves as the Greater Scope Villains of The Legend of Korra as a whole, but to a lesser extent with Book 1. They attempted to kidnap Korra as a child, which resulted in her being isolated from the rest of the world for the past seventeen years of her life. When Unalaq was a member of theirs, he learned of Raava and Vaatu; he also engineered the Red Lotus' attempt to kidnap Korra, resulting to Zaheer and his gang getting captured and continuing his new plan in becoming a Dark Avatar. Their murder of the Earth Queen also gave rise to the Big Bad of season 4.
Batman: The Animated Series: Salvatore Valestra, a mobster who forced Andrea, one of Bruce's love interests, to leave the country. Without her, Batman ended up alone and took the cowl to become Batman. Ordering the death of Andrea's father led to the events of Batman: Mask of the Phantasm; the man he hired also led to a fair share events in the present, since the man would ultimately become the Joker.
While Lawrence Lactavius Limburger is the main antagonist of Biker Mice from Mars, he occasionally answers to Lord Camembert, who is the leader of the Plutarkians and is therefore indirectly responsible for the Plutarkians devastating Mars and Limburger's schemes to strip-mine Chicago and wipe out the three titular Biker Mice.
Code Lyoko: Project Carthage is a military operation Franz Hopper and his wife were once a part of that they left when they felt it became too unethical. When they took his wife, leaving him and his daughter alone, he created XANA to combat them. Instead, XANA imprisoned them both and developed sentience in a bid to destroy humanity.
Codename: Kids Next Door has Grandfather, the Big Bad of The Movie, and the father of the series-wide Big Bad, Father. He's the reason why Father is the way he is, and his actions prior to the series eventually facilitated the founding of the Seventh Age of the Kids Next Door by his other son, Numbuh 0 a.k.a. Monty Uno, Numbuh 1's father.
Danny Phantom: Pariah Dark is the King of all Ghosts, feared and hated by them. He's only faced Danny once, due to how he was freed from his Sarcophagus of Forever Sleep, but his reign is still one the denizens of the Ghost Zone feared.
In the Dungeons & Dragons animated series, one episode featured Big Bad Venger's master, an insanely powerful Eldritch Abomination that appears and starts destroying the entire realm. Even at the end, when it's banished with the combined efforts of Dungeon Master, Venger, and the Heroes, DM still remarks that what they've accomplished is but a temporary victory.
Ed, Edd n Eddy: Though the show is about Eddy using his friends to scam the neighborhood for jawbreaker money and the kids, though not entirely pleasant, are just trying to deal with his antics, the Grand Finale reveals the older brother he speaks so highly of was a cruel bully whose treatment of Eddy made him the person he is.
Final Space: The Titans, a group of ancient Eldritch Abominations that bring chaos and destruction to the universe. Lord Commander is acting under the assumption that he is some sort of Chosen One and will ascend into titanhood if he manages to use Mooncake to open a portal to their dimension and bring them to the universe.
Generator Rex has the Consortium, who are the reason for the nanite event.
Gravity Falls: We first meet Bill Cipher as a seemingly-all-powerful demon who has no problems working with Gideon Gleeful as long as Gideon helps him with a mysterious plan in the future. He only appears directly in the penultimate Season 1 episode, "Dreamscaperers", but hints at a darkness approaching far beyond anything Gideon could come up with. Come Season 2, he makes good on his promise, unsurprisingly reveals himself to be said darkness; he then becomes the Big Bad personally, and Gideon is Demoted to Dragon.
Grojband has Mayor Mellow, despite not being a villain.
On Invader Zim, Zim could probably be seen as the Big Bad focusing on Earth, with the Irken Empire itself (including the Tallests and Control Brains) as the Greater Scope Villain out to conquer the rest of the universe, especially since technically Zim conquering Earth wasn't even part of the Empire's plans.
Jumanji: The Stalker is the entity behind the game who ensures that people will play it and seems to be the being who maintains order with all of its creature and villains.
Justice League: Brainiac for the Cadmus Arc in Unlimited. Having used Lex Luthor as a body to hide in since Superman: The Animated Series, Brainiac has been subtly influencing Luthor since by granting him super strength, greater intelligence and curing his kryptonite-induced cancer. He had also affected Luthor's actions, making him use Cadmus' resources to construct a new body for him. When that failed, they stole a piece of alien tech from Cadmus called the Dark Heart and fused into one being to use it to reshape the universe in their image.
Kat is the main villain of Kid vs. Kat, but-as the name implies-he answers to the Kat Kommander, the alien who sent him to Earth to Kill All Humans.
While League of Super Evil centers around the schemes of the League, Skullossus is the most threatening villain to the world at large.
Scar, the long-dead Big Bad of The Lion King, serves as this for The Lion Guard. His great-nephew Kion succeeds him in leading the titular Lion Guard, but is constantly worrying about ending up power-mad and destructive like him. In Season 2, however, Big Bad Janja decides to resurrect him to gain his help in taking over the Pride Lands, with Scar's spirit now serving as the Big Bad of the season after assembling an army of the show's Rogues Gallery.
Horde Prime, mainly in She-Ra: Princess of Power since the Horde was her primary enemy. The master of both Hordak and Skeletor, Prime almost never played a direct role, but would occasionally appear to berate Hordak for his constant failures.
Hordak himself is the Greater Scope Villain in He-Man and the Masters of the Universe (2002). He plays a prominent role in the backstory as the Arch-Enemy to King Greyskull (and oddly enough to fellow archvillain King Hiss as well) and the one who transformed the dying Keldor into Skeletor. In the series proper he is a Sealed Evil in a Can who only briefly appears as gigantic cloudlike apparition during an attempt to release him only to fade away once the attempt is foiled. Had the series continued Hordak would have been freed and become the Big Bad proper for a season before being defeated by Skeletor. Also, Hordak is the one who divided that series' version of Eternia into the Light Hemisphere and the Dark Hemisphere.
Hordak is also this in She-Ra and the Princesses of Power, though in this case, it's because he's too preoccupied with his science experiments and generally running the Horde to ever directly face any of the heroes. His underlings, like Catra and Shadow Weaver, do most of the fighting for him.
Bravestarr used the exact same format, with Big Bad Tex Hex answering to an ancient entity called Stampede, who was the one who found him dead after his fatal crash and brought him back as an undead servant, leaving Tex no hope of ever being his own master again or turning back.
In Mighty Max, the series' main villain the Skullmaster mentions that he has a master of his own, but his superior is never seen at all throughout the run of the series.
The Pirates of Dark Water: While Ren and his crew are traveling to find the thirteen treasures of Rule to destroy the Dark Water, dealing with Bloth and his crew wanting the treasure to control it, they are too busy to deal with The Dark Dweller that created the dark water to consume their world.
Aku himself became one in Season 5. Sure, he's still the chief antagonist, but a lot of antagonists have more involvement than himself in the plot such as Scaramouche (Aku's favorite assassin), the High Priestess (the woman who raised the Daughters of Aku), the Dominator (a brutish, tyrannical man in Aku's employ) and Lazarus-92. On the other hand we have the Omen and Jack's Inner Self later revealed to be his Evil Counterpart,who serve as a more psychological threat to Jack. So yeah, Aku never directly acts against Jack (at least until "C"); instead, it's the other mentioned characters that cause trouble for Jack.
Scooby-Doo! Mystery Incorporated featured a slew of villains, from Professor Pericles, to Mr. E, to Mayor Jones, and yet all were unaware that they were pawns corrupted by the influence of The Evil Entity that was encased in a crystal sarcophagus, waiting for someone to to set it free.
The Smurfs have to constantly fight Gargamel's schemes, but even he seems nice in comparison to evil warlocks Balthazar and Nemesis, to the point that they end up in Enemy Mine situation with Gargamel against them in some episodes.
Elena and the Secret of Avalor , a crossover tv-movie between Craig Gerber's two shows, Sofia the First and Elena of Avalor , has Shuriki as the main antagonist. Sofia got her amulet, which Cedric spent two and a half seasons getting, when the titular protagonist of the latter show was trapped in it by Shuriki after her parents were killed . Sofia's mission is to free Elena and help her take back Avalor. They succeed in taking back the kingdom, but the ending sets up Shuriki to be the Big Bad of the latter series.
Edwin Alva in Static Shock was the corrupt corporate executive responsible for unleashing the Big Bad gas. While a jackass in person and the antagonist of a couple of episodes, he is unwittingly responsible for causing the explosion that created superhumans (it was provoked by circumstances beyond anyone's control given it was a police shootout between gangs), the show's actual Big Bad Ebon would not have been created had it not been by Alva's influence.
Toffee makes his entrance into the show in "Fortune Cookies", joining the ranks of Ludo's army, and easily proves to be infinitely more dangerous than Ludo and his minions combined. By the episode "Marco Grows a Beard", Toffee throws Ludo out and steps down to Big Bad status. After seemingly dying in "Storm the Castle", Season 2 reveals that he became Ludo's new sentient wand and was pulling his strings all along, reverting to his role of Greater-Scope Villain while Ludo regains the Big Bad title... until the final few episodes, where he loses his position to Toffee once again, who cements himself as the Big Bad for the forseeable future.
Queen Eclipsa has made no physical appearance barring a blink-and-you'll-miss-it cameo as a crystalized prisoner, but Season 2 builds her up as a threat as big as Toffee himself, especially since it's her chapter in the spellbook that prompts Star to learn more powerful magic... with some dark implications. Her chapter is also responsible for Ludo becoming possessed by Toffee once the former reads it.
In Star Wars Rebels, Darth Vader and the Emperor, The Dragon and Big Bad of the original trilogy, serve this since the first season's Big Bad, The Inquisitor, merely works for them. In Season 2, Vader becomes the Big Bad, but steps back once he accomplishes his mission at the end of that season that being the presumed death of Ahsoka Tano, later revealed to be alive. Grand Admiral Thrawn becomes the Big Bad of Seasons 3 and 4, with Vader and Sidious once again as the GSV's until the finale, in which Sidious personally menaces the heroes, specifically Ezra (albeit with Thrawn remaining the main direct threat).
Steven Universe: The Diamond Authority that leads the intergalactic Gem Empire that Rose Quartz and the Crystal Gems rebelled against before the series began. We become aware of the Gems' alien origins by the middle of the first season, but we only properly learn of the Diamond Authority in the following season. The members of the Authority are seen sparingly. Yellow Diamond was first shown in season two and has only been in four of the show's 140+ episodes. With her in charge of the military, most of the villains seen throughout the show, such as Jasper or Aquamarine worked under her orders. Blue Diamond didn't appear until the fourth seasonnote a shadow cut-out version of her appears in a season two episode, however, and White Diamond didn't appear and wasn't even mentioned until "Legs From Here to Homeworld", with only the symbol of the group, a stylized mural, and her silhouette and hand in Garnet's flashback in "Your Mother and Mine" alluding to her existence before then. Pink Diamond was the one in charge of colonizing Earth, which lead to the aforementioned rebellion and her supposed shattering at the hands of Rose Quartz. She first appeared in person during a dream sequence in season five, and later the Wham Episode "A Single Pale Rose" reveals she actually faked her own shattering and became the main character's mother, Rose Quartz.
Super Robot Monkey Team Hyperforce Go!: The Dark Ones were an Eldritch Abomination race responsible for the Big Bad, the Skeleton King. They corrupted him when he used to be the alchemist that created the Robot Monkey Team. One of them, a giant worm, merges with the Skeleton King and goes into space to consume worlds, and destroying it is the driving force of season 3.
Teenage Mutant Ninja Turtles (2003): The Demon Shredder was the inspiration for Ch'rell, the Utrom Shredder, and his reign resulted in the creation of the Ninja Tribunal, whose servant adopted Hamato Yoshi, the Utrom Shredder's eventual victim, which in turn led to Yoshi's pet rat Splinter and four baby turtles to being mutated. Five of his minions were enslaved by the Utrom Shredder, but once he is defeated and they break free, they start reviving their master and he steps down to Big Bad status for season 5.
The 13 Ghosts of Scooby-Doo: Asmodeus, introduced in Scooby-Doo! and the Curse of the 13th Ghost, is retroactively this to the series. The king of demons and Vincent Van Ghoul's evil ancestor, his corruption and rise to power is what brought about the Chest of Demons being made and to seal the evil spirits within. Since the Asmodeus featured is a fake, it's left ambiguous what became of the real one. Though she refuses to believe anything supernatural happened, Velma suggests the real Asmodeus may have sought to act as Vincent's guardian angel as a means of redemption.
The Big Bad Mumm-Ra of ThunderCats (both the original and 2011 reboot) is a servant of the Ancient Spirits of Evil, who grant him his power in exchange and who establish their presence non-verbally only through their hideous giant statues, with their eyes glowing whenever they respond to Mumm-Ra's requests.
Total Drama has an interesting case with Chris. Unlike most Greater Scope Villains, who hide in the shadows, Chris is front and center and even appears in the most episodes of the entire series by a long shot. However, his role is precisely to stir up drama for ratings. Whenever contestants begin to form genuine bonds, Chris always steps in to force a conflict on them. Heather may have been the Alpha Bitch of Season 1, Courtney may have abused Screw the Rules, I Have Connections! in Season 2, Alejandro may have pulled an Eviler Than Thou on the previous villains in Season 3, Scott may have been a Team Killer in Season 4, etc., but these characters are simply The Heavy of each season. Chris is the one always there gleefully making the contestants' lives miserable. To make it even worse, he is basically always a Karma Houdiniuntil the finale of Season 4, when he finally gets put in prison for the insane amount of ecological damage he caused.
Dr. Killemoff of the planet Smogula was the main villain of Toxic Crusaders, a cartoon loosely based on Troma's The Toxic Avenger film series, but it was established that he's polluting the Earth because of orders from the Smogulan leader Czar Zosta.
Unicron of Transformers is the ultimate evil in the metaseries, but is usually a distant figure, with Megatron (or his replacement as Decepticon leader) being Big Bad. In Transformers Prime he's mentioned as early as the pilot episode as the source of Dark Energon, which plays a considerable role throughout the series, before finally taking over as the Big Bad in the finale movie Predacons Rising. The exceptions are Transformers Armada, where Unicron is the Big Bad all along, orchestrating the conflict for his own purposes, and The Transformers: The Movie, where he serves as the Big Bad with Galvatron as both The Heavy and The Starscream. The Transformers revealed in the third season that Unicron was the creation of an alien scientist named Primacron, which meant that Primacron was indirectly responsible for the conflict in The Movie.
Gunmar the Black from Trollhunters. The big-bad Troll King of the Gumm Gumms and master to nearly every Big Bad in the series.
Argante, an eldritch witch of some kind, is, potentially, another. Other than a somewhat random appearance at the beginning of an episode that explain Angor Rot's past, not much about her is known. And yet, her sinister presence wafts through tout the first Season's second half through Angor Rot, a presence that has long-standing implications.
The Order of Janus/Janus Order, an umbrella Order for all Changinglings and their affairs, could also qualify as a third.
Due to it being a spin-off of TRON: Legacy, TRON: Uprising has the former's Big Bad, Clu, in this role. His takeover of the grid is at the heart of the conflict in the show and all of the villains answer to him, but never confronts Beck.
Villainous interestingly depicts Black Hat as this in relation to every Cartoon Network Big Bad. The Phase Two orientation mini-series acts as if all the Cartoon Network shows are connected and most of the villains have done business with the Black Hat Organization at some point or another and while Black Hat is treated as a greater threat than most, if not all of them, he never directly antagonizes their respective heroes.
Wander over Yonder has Lord Dominator, who's been described as such as a better Hater than Lord Hater according to the series' creator. She becomes the Big Bad proper in the second season.
The Three Ancestral Witches, especially in seasons 1 and 3. Being responsible for the destruction of Domino, they are the cause of many of the series's problems. The Trix, their descendants, take over their role to conquer the magical universe, and Valtor was their creation and servant. At the end of season 3, they attempt to directly control Valtor to their will, but he's killed before he can do anything. They become more involved in the movies.
Season 6 has Acheron, a dark wizard residing in the Legendarium (an ancient book) and is the true person behind Selina (that work with the Trix. but is a Dragon with an Agenda). He was the one who granted Selina power in exchange for working to free him from the book.
Darkseid was revealed to be this in the finale of Young Justice, being the secret collaborator with The Light, and the show ended before he could take a direct role. When the series was uncancelled, his status as this was reinforced in the episode "Evolution". Darkseid's invasion of Earth long ago and the deal Vandal Savage made with him at the time to spare Earth (they would conquer the galaxy together before fighting one final conclusive battle against each other for all of it) is the driving force behind Vandal Savage creating The Light in the first place. Everything Vandal did as the founder and leader of The Light was done to forge Earth into a galactic superpower that could take on Apokolips.
My Little Pony: Friendship Is Magic originally tinkered with such an idea by having Nightmare Moon return because "the stars will aid in her escape", with Lauren Faust entertaining the idea that something was responsible for corrupting Nightmare Moon. However with her departure from the series, the show seemingly abandoned this idea and turned Luna into The Atoner who fell purely due to her own jealousy, while the comic series went another way and had the small-time "Nightmare Forces" be responsible for her (and later "Nightmare Rarity's") corruption. But latercomics subverted that: Nightmare is actually The Virus, with Luna (and later Rarity) forcibly turned into her main vessel(s) and the Forces as innocent Dream Weaver aliens forcibly turned into sub-vessel Mooks.
Discord created the plunderseeds, the extent of the damage of the later is unclear, but in the very least they were the antagonist in one episode and not Discord.
Stygian became the Pony of Shadows after he was corrupted by the Well of Shadows. Who created the Well of Shadows remains a mystery, but they probably weren't good.
Season 9 reveals us Grogar, the ultimate villain of the entire show. He is an Ancient Evil who ruled Equestria with an iron fist, until his defeat at the hands of Gusty the Great. Now, bent on reclaiming Equestria for himself, he created the monsters that attack Equestria. He is also The Man Behind the Man to most of the Big Bads that Mane Six have faced. He does not appears in the show until the Season 9.