David Xanatos from Gargoyles is usually one step ahead of the Gargoyles, and everyone else. He frequently got away with actions that would send a normal man to jail for the rest of his life (although he was jailed for a short time), and was a member of the Illuminati's guild. Since Xanatos was such a smooth talker, he would make you believe he was your friend all while positioning the knife in your back.
He might adequately be described as Lex Luthor (Evil Corporate Mastermind) mixed with Doctor Doom (genius inventor and likes mixing magic with science), only handsomer, possibly richer, and with none of the flaws that cause their plans to collapse, namely ego inflation issues and revenge obsessions.
Uncannily enough, his FIRST second LINE in the show is "Magnificent!"
During the first story arc, Xanatos is "defeated" and sent to the slammer. Unfortunately, this means he has nothing to do all day EXCEPT formulate new plans within plans. . .
Xanatos's creation, Thailog, is one as well, solidified when he betrays and then outwits his maker in his very first appearance, leading a fearful Xanatos to speculate that Thailog may be even smarter than he is. Going by the comic continuation, Thailog seems to have inherited his father's fondness for schemes that profit him no matter the outcome as well.
Xanatos's wife, Fox, who also managed to outsmart him on one occasion. He even refers to her as his equal!
His proposal amounted to "We get along, we'll have good kids, and we're the only ones as smart as each other."
Megatron of Beast Wars: He's a user and abuser of his followers, a gloating sadist who enumerates the ways he's beaten his enemies as he's standing over them in his moment of triumph, a master manipulator who is only served by his underlings' treachery... and yet he carries off scheme after scheme with audacity, panache, and an almost vaudevillian flair. Nor does he work in small potatoes; his schemes include two bids to rewrite history as well as consuming his namesake's spark to add to his own personal power. Magnificent. Bastard. Yesss.
He singlehandedly took over Cybertron and devoured the sparks of his entire species and became a GOD in the (contested) sequel series.
If nothing else, his apparently keeping Tarantulas and Blackarachnia around simply so he can keep his wits sharp by predicting their betrayals would qualify him for this trope.
By surrounding himself with betrayers, he gets to cackle as he watches them backstab one another and stay in the position of power. And it's damn entertaining to watch.
At one point, Terrorsaur has manage to seize command from Megatron. During a crisis, Megatron escapes from the cage Terrorsaur has locked him in. How does he reclaim his authority? He steps up and... does nothing. He lets Terrorsaur stay in charge just long enough to totally humiliate himself, and then takes the stage to give a summary of the failure and mockingly ask if anyone still wants to take orders from Terrorsaur.
In the Botcon exclusive story "Reaching the Omega Point," by Simon Furman, the tyrant Shokaract - who has all the powers of the Dark God Unicron - travels back in time to the Beast Wars, and beats the crap out the most powerful Transformers in existence with ease. What does Megatron do? He tries to BLACKMAIL Shokaract, threatening to destroy the "Dark Essence" that the demigod had come to protect. He fails, but provides a crucial distraction that ultimately dooms Shokaract.
His Transformers Animated counterpart also comes close, if not equal with him. This guy manipulates Sumdac to repair his body, avoids the mistake of his predecessors by killing Starscream the first chance he gets, coaxed the Constructicons into his employs with just a couple barrels of fine oil, and he Out-Gambitted Starscream to ensure that the Omega Supreme clones didn't imprint on Starscream or Megatron himself, but on the loyal Lugnut. And when he got physical, he got physical. In a rather defining moment that puts him in this trope, after receiving the Allspark Key which grants him a new body, he subsequently pummels Optimus Prime and the rest of the Autobots. When Optimus effectively tells him to bring it on because he won't give up the location of the Allspark, Megatron reveals he already has the Key which will lead him directly to it and that he was only kicking the crap out of Optimus for his own amusement.
Really, his only mistake was not figuring out a way to kill Starscream after it became clear that normal methods weren't working, an incident which rather clearly fell under Rule of Funny.
This Megatron is so incredibly cool that he doesn't even bother to remember any of the main Autobot's names unless it suits him (i.e. when he captured Bulkhead and when he fought Optimus Prime one-on-one in the final episode). The reason why? He does not consider any of them to be any threat to him. Only when Optimus fights him one-on-one in the Grand Finale does Megatron seem to regard him as being above the status of '"annoyance" and equal to "Worthy Opponent".
Impostor Dan, from Dan Vs. After stealing Dan's identity, and endearing himself to everyone in town, he is finally taken down by Dan. Being a Magnificent Bastard, he gets out of prison and becomes a telemarketer. He uses his position to drive Dan insane, using a hidden transmitter to act as the voice inside his head, renting an apartment, just to capture them both, and knowing the characters so well that he can place traps exactly where they will be. When Dan chases him with a baseball bat, he gets a cop to taser him twice. He even manages to do all this while being completely likable, suave, and normal.
Megabyte from ReBoot. The low, British baritone voice of Tony Jay certainly helps, but this is one of the few cartoon villains that has never suffered from any sort of Villain Decay, and is actually considered more dangerous as the series progresses. His most magnificent moment (besides the guitar duel) is when he took advantage of the web invasion and subsequent Enemy Mine situation to strand Bob, Mainframe's champion, in the web. While Daemon is more powerful and dangerous, Megabyte's return in season 4 evoked much more fear from the main cast. What makes this so Magnificent is how his dispatching of Bob is so un-magnificent. He shoves him and presses a button. Dead easy. It also helps that judging by the season four cliffhanger, he wins.
Megabyte's bastardy in the first few seasons was completely overshadowed by what he got up to in the fourth season. At this point, he has decided to forgo his pursuit of power in favor of personal revenge, which he does in truly epic fashion. He uses his newfound Voluntary Shapeshifting to return to Mainframe in the guise of the original (Season One/Two) Bob, and comes within literal seconds of marrying Dot just to mess with everyone's heads.
She also read from Zuko that Aang was not necessarily dead, and left the potential failure on his shoulders. Although that could be drifting towards another trope...
Azula is succeeded by Amon in The Legend of Korra, who has obtained this status in record time, SIX EPISODES! Every thing this guy does only gains him more followers. He sends a threat to city hall, and knows that they won't listen and just heighten security at the Pro Bending arena. He then has his fellow equalists disguise as simple audience members and sneak in their weapons by hiding them in their popcorn. Turns out he wanted the entire police force there so he could take them all out at once before they could stop him and show the whole stadium how powerless they were. He also might have paid off the Pro Bending referees to not call out the Wolfbats team's cheating to ensure that they'd win the match, so Amon could then make an example of them by taking away their bending. And he knows how to take advantage of the situations: he always makes sure that people see the truth of his extremist beliefs that benders abuse their powers. It helps that the first thing we ever see him really do in the show is taking bending powers away from dangerous crime bosses.
Technically, he may have achieved this status in THREE episodes, because although he achieved it by the end of Episode 6, he didn't appear in Episode 1, 2, or 5. Yes, this entire feat was accomplished in just three episodes. (Technically, he does appear in the first episode, but just at the very end merely saying "I'm going to put my plan into action now", so he doesn't really do anything until episode 3.)
His plan in episode 6 was actually a win/win for Amon. If they do listen to his threat and stop the Pro Bender finals, then the government and police force look weak and useless against him and his Equalist movement. If they don't listen to his threat, well, we saw what happened when they didn't.
And to cap it off, in the finale, we see that he wears incredibly convincing makeup under his mask to make his face look massively burned and scarred, just in case anyone called him a liar or his mask got knocked off.
Korra Book Two brings us Varrick, the goofy, charismatic Uncle Pennybags of an executive who befriends our heroes in the first few episodes before talking them into helping him escalate a regional conflict into a full-scale war, smuggle in weapons, organise a small military coup, and buy up everything they own whilst still keeping them completely convinced that he's on their side. As he cheerfully puts it, "If you can't make money during a war, then you just plain can't make money!" By the time anyone finally realizes he's only out for himself, he's already succeeded in stealing all of Asami's remaining goods then convinced her he's "saved" her company by buying it out. He then gets the only person who suspects him thrown in jail, and, if Bolin hadn't happened to spot the boat left by his soldiers, he likely would've succeeded in kidnapping President Raiko and convincing Republic City to send troops to the war front, earning him even more money. Even when he's jailed, he's not phased by it, since his company made the prison and he designed himself a Luxury Prison Suite in the likely event he ended up in there. He then lends the Krew his personal battleship as an act of goodwill. He ends the season escaping justice by taking advantage of the chaos Vaatu is causing and using a hang-glider which he just happened to have smuggled into his jail cell in the event an aerial escape opportunity presented itself. Throughout the season Varrick manages to be surprisingly ingenious in his plots, Crazy-Prepared for any eventuality, and genuinely affable to the Krew even as he's manipulating them or screwing them over for his own interests.
Nerissa is hands down the best manipulator in the television series. Her schemes have spanned over ten years to complete her goal of universal conquest to unite all words, Nerissa takes on multiple false identities to help defeat Meridian's evil dictator by posing as a castle servant to pass information to the rebel army.
Conceived a child who she never raised to lead that same army. Manipulated minor villains to distract the heroes under the guise of wanting to assist them while she worked behind the scenes. After the rebellion won, she maintained her disguise as a loyal servant of the queen, only to steal her powers for herself.
Nerissa only really lost because she became obsessed with power and started making stupid mistakes in pursuit of more of it, in addition to Will becoming something of a Magnificent Bastard herself by releasing Phobos from prison with a binding magical promise to not keep Elyon's power for himself. It would have worked, too, except for Cedric guessing the plan and turning on Phobos just before he fully broke the promise.
Aladdin: The Series has Mozenrath, comparable to Jafar from the Aladdin movies. (See also the film example section.) Even though the confidence was always there, Mozenrath was able to back up his smugness from the get-go. His very first plan involved using Genie as bait for a magic-devouring monster, in order to make Aladdin capture it for him, thus setting up a simple but yet effective Xanatos Gambit. While it didn't last for long, Mozenrath did indeed end up with the beast under his control. Aladdin and his friends did face many capable enemies during their adventures, but Mozenrath was the one who really made them sweat, always pulling something from his sleeve to put the odds back in his favor. If that wasn't enough, the lad was also blessed with a silver tongue that really got our heroes on the nerves. Really, he spends one episode just sitting on his throne, snarking and gloating to a locked up Aladdin, and it still didn't end in a complete loss for him. After all, there's a reason why he's the only villain to ever hear Aladdin say the words "You win".
Mozenrath was, in fact, so dangerous, that Aladdin and Jasmine once tried to sneak into his fortress without asking for Genie's help or even telling him about it. (The reason being, the place had powerful anti-magic defenses, and they knew Genie would have blown their cover badly.) As you might expect, Genie finds out and tries to help anyway... Aladdin and Jasmine's precautions were not without merit.
Dogbert on the series Dilbert whose "religious belief" is "that everyone exists for the sole purpose of entertaining me." On one episode, he sets up a carnival booth where you "knock a street urchin off a beam with a baseball and win a toy." In another, he convinces Congress to abandon all holidays in favor of National Dogbert Day (The traditional Dogbert Day feast: the bald eagle. He wanted something special) for the sole purpose of being annoying. (The same reason he invented Secretary's Day.) Also, the aptly named Bob Bastard, the caped and hooded company tester on a quest to crush the hopes and dreams of engineers.
Dilbert: I'm sorry Alice, but he's the embodiment of all that's horrid and loathsome in this world.
Alice: Just because it's written on a bathroom wall doesn't mean it's true.
Tombstone in The Spectacular Spider-Man proved himself to be this upon his very first encounter with Spider Man. He floors the webhead in one swift move, antagonizes him by telling him how he is fighting a losing battle, uses it as an attempt to get Spider Man to do what he wants and finally makes Spider Man look bad in the eyes of the cops. All in around five minutes.
Dr. Octopus as "The Master Planner" has also obtained this status. He operates his plan, for the most part, from a mental ward, has Gwen Stacy kidnapped and then has her father betray the law in exchange for her safety, nearly takes over the world in the end... all while managing to casually sit back and drink coffee out of a mug labeled "Evil Genius".
Norman Osborn is also up there, playing both sides throughout season 1—getting paid to make supervillains to fight Spider-Man, and then getting paid to come up with the systems to contain them. In season 2 this continues, plus in "Accomplices" he carries out a beautiful plan wherein he gets the competition to demolish each other fighting over what is, ultimately, a worthless chip—earning himself half a billion dollars with no risk or effort. Oh yeah, and he was the Green Goblin all along, willing to break his son's leg to fool Spidey.
Danny Phantom has an intriguing one: Vlad Masters/Plasmius. He wants to marry Danny's mom, adopt Danny and kill Jack, not exactly in that order. A lot of his lesser plans work, but the main ones probably would if he had better control of his emotions and kept his priorities straight.
For a more straightforward example, there's "Reign Storm" where Vlad's biggest plan then succeeded in spades, manipulating nearly everyone to get what he wants by end.
For even more examples, it can take several rewatches of the show to understand Vlad's plans and just how many of them he has. A couple of great examples include the fact that Vlad actually sent many of the ghosts Danny fought shortly after gaining ghost powers and the surveillance footage he received from Valerie's suit to clone Danny.
Darkseid from the Superman: The Animated Series and Justice League. Even though Superman usually won the day, he took every defeat (and victory) with the same steely expression. Even when Darkseid was beaten on his own planet, Superman threw his body to his slaves on Apokolips and said they could do whatever they wanted to with him. The slaves began to pick up their cherished leader and take care of him. While being carried off, Darkseid gave a confused and horrified Superman a parting line:
"I am many things, Kal-El, but here...I am God."
Arguably just as impressive (even if it didn't succeed) was his brilliant Evil Plan in the Justice League episode, Twilight: Playing Both Sides in the conflict between Superman and Brainiac. He successfully manipulates both Superman and Brainiac into believing he's on their side, pitting them against each other and playing both sides. He boxes them both into this even though both Superman and Brainiac know that they can't trust him and know that he'll betray them. But appealing to Superman's (and the Justice Leagues') sense of morality and Brainiac's self-preservation he does it. By the end, Superman is incapacitated and Brainiac is under Darkseid's control with him moments away from achieving his ultimate goal. Only the last minute arrival of Batman, Wonder Woman, and Orion (which nobody could've forseen) foiled him.
"President? Do you have know how much power I'd have to give up to be President? That's right, conspiracy buff. I spent $75 million on a fake presidential campaign. All just to tick Superman off."
Slade from Teen Titans normally falls on the Smug Snake side of things, due to his overconfidence and habit of grabbing the Villain Ball at inopportune moments, but in the three-part season finale "The End" he graduates to full Magnificent Bastard by orchestrating the downfall of a nearly all-powerful demon at no real cost to himself, getting his humanity back (which was his main goal all along) and doing it with style. Being voiced by Ron Perlman helps.
Demon Warrior: "Fool. You cannot hope to defeat pure evil!"
Slade: "Actually, I'm not such a nice guy myself." (activates hidden explosive and blows demon to cinders) "Don't bother getting up. I'll let myself out."
A more straightforward example would be Tak, who would have succeeded if the Villain Ball hadn't made her brag to Zim.
Derek Powers from Batman Beyond. Manipulated a city with his company, and only grew more deadly when he gained radioactive powers. Using his money, intel, and connections, he kept people under his thumb and proved to be a deadly opponent for the new Batman.
His son Paxton also qualifies, arranging for his father's exposure to the public and eventual demise despite Batman's best efforts to stop him. He does next to nothing in Season 2, but then again, why bother? He had already won in his first appearance!
V.V. Argost from The Secret Saturdays. Bold, manipulative, cunning, and brilliant, a master of misdirection with a showman's flair, more often than not he wins by the end of the episode and has proven to have a large array of technology and knowledge, as well as in impressive collection of cryptids and ancient artifacts, in his goal to Take Over the World. Indeed, he succeeds so well that it proves to be his undoing, as he is killed when he absorbs two forms of supernatural power which prove incompatible.
Gibbs from Titan Maximum manages to be this in addition to being a real Smug Snake thanks to the main heroes being a bunch of idiots who don't always know what they're doing.
Mojo Jojo can be this at times. While his plans tend to be hair-brained, sometimes he's shown enough savvy and manipulation to casually perform things that people rarely notice until they happen (the "Powerpuff Girls Rule!" special is a fine example.) The movie played this straight.
There's also HIM, who always means business when dealing with the Girls. He tends to end up doing something that involves manipulating one of the Girls' feelings (Bubbles) or something on the grand scale.
Palpatine's responsible for engineering this massive war and will win regardless which side triumphs, either with the Republic as the Chancellor or the Separatists as Darth Sidious, with a powerful new sith follower (either Dooku or Anakin) as icing on the cake.
Ed Wuncler Sr. from The Boondocks is a combination of this and The Chessmaster. This is a fat, rich old man, who would normally not be the least bit threatening but look at all he's done:
He opened a restaurant using illegal workers and Robert as his Unwitting Pawn, knowing full well the restaurant's food was so addictive it would turn the nearby park into a cesspool of crime, thus lowering the property values so he could buy the land for dirt cheap.
He tricked Jazmine, a 10 year old girl who started a lemonade stand, into being partners with him and then made it so that she ended up owing him money and allowed him to sell his own cruelty free lemonade.
He had his grandson Ed III and Ed's friend Gin Rummy break into people's houses so they'd buy his security system.
He not only had a girl fake a serious injury so Huey would quit the kickball team, thus restoring the curve, but then blackmailed him to play again.
Finally, he had Ed and Rummy set up a bomb in one of his buildings, and then calmly reveals when Huey and super agent Jack Flowers foil this plot that it was designed to inspire patriotism, sell merchandise, and make a movie about an obnoxious security guard who would have died in the explosion. And to top it off, when Flowers counts down 3 seconds before he shoots him, Wuncler calls PRESIDENT FUCKING OBAMA to stops him, then calmly tells them to let themselves out. And does all of this just by being crafty, evil and obscenely wealthy. Magnificent Bastard indeed.
Carmen Sandiego. In the mid-90's cartoon version, Where on Earth Is Carmen Sandiego?, she was as slick and suave as a female James Bond, but would steal priceless artifacts either just for the thrill or for a huge not-so-evil plan (in one episode, she stole several rare statues to make the worlds largest chess game) and would constantly bait and taunt the two detectives trying to catch her, all for the sport of the hunt (even though she was the prey.
Chase Young from Xiaolin Showdown, mostly during the second season in which he debuted, would meticulously manipulate events so that even if the monks won, Chase would benefit from it, mostly with regard to his plans to corrupt Omi. This lead to him, on several occasions, helping the monks in order to gain Omi's trust, as well as manipulating other villains to force Omi into situations where he would have to resort to underhanded tactics not approved of by his friends.
Alejandro from Total Drama World Tour; at least by the usual standards of Total Drama. He manipulates more successfully than other antagonists in the past, and is responsible for more eliminations than anyone else.
Total Drama's original manipulator, Heather, is arguably able to match him (and beat him, in the US ending) in the same series.
Mike's hidden alternate personality, Mal, from Total Drama All-Stars is another example by Total Drama standards. He imprisons Mike and his other four alternate personalities inside his own subconscious and is able to impersonate Mike with the only person to be suspicious of him being Duncan, who nobody believes. He later plays everyone (especially Zoey) like a fiddle post-merge and orchestrates nearly every single elimination whether by sabotage or manipulating others. Zoey later found out about Mal and he noticed her change of attitude and knew he had to win a challenge to save himself but even after Zoey figures out about Mal and wins the challenge, she still takes him with her to the finale (even if she only chose him hoping she can get Mike back).
In The Simpsons, the organized crime community as a whole shows signs of this, but outside of the organized crime community there's also Sideshow Bob, and the Springfield Cat Burglar.
Krusty Gets Busted, in which Bob frames Krusty for armed robbery, and takes over Krusty's show. He manages to convince almost everyone of Krusty's guilt, except for Bart and Lisa, who just so happen to uncover the whole scheme when Sideshow Bob says he has big shoes to fill.
Black Widower, in which after being released from prison, Sideshow Bob convinces every Simpson except Bart that he has reformed. Bob then marries Selma Bouvier, who has made a lot of money in the stock market, so as to inherit her money. Bob also finds out that Selma tends to smoke after watching MacGyver, and that she has an impaired sense of smell. So he then decides that one day, to get the money, he will get up and leave while she is watching MacGyver, and leave the gas valve open so as to fill the room Selma is in with natural gas, without her noticing, such that when she lights up to smoke her cigarette when the show is over, the ignition will blow up the room she is in, killing her and leaving him with her money. The only reason this does not work is that Bart, who was already distrustful of Bob, also knew these things about Selma and managed to guess what Bob's plan was.
Cape Feare, in which Sideshow Bob manages to convince the parole people that he has reformed. Upon hearing of his release, the Simpson family flees Springfield to a houseboat in Terror Lake, but Bob manages to find their houseboat anyway. While the family is asleep, Bob disconnects the boat from the dock, and ties up all the Simpson family except Bart, including the pets. Then, cornering Bart at the edge of the boat, Bob is going to kill Bart until Bart convinces Bob to sing the entire score to H.M.S. Pinafore first. By the time Bob is finished singing, the boat arrives in Springfield, where the police are waiting for Bob and have him arrested.
Between all the Organ Theft, kidnapping and extortion, Murdoc definitely has his moments.
Rava from Galtar and the Golden Lance. When she's assigned to take down Galtar, she actually succeeds in capturing him, and only ultimately loses because she also used the assignment to set Tormack up, she tried to pull an I Have You Now, My Pretty and imprisoned Galtar when he refused, and Tormack and Galtar pulled an Enemy Mine to restore the status quo. In a series where the villains tend to be generally a touch more credible than most similar action cartoons of the age, Rava is still the most dangerous of them all.
The second season features the machinations of the Skrull Captain America, who really utilizes people's trust in Cap well in order to further the Skrulls' plot for Earth. Preying on the Avengers' trust in the real Cap to keep them under surveillance without Iron Man to get in the way of plans, as well as dealing with the Hulk by having him voluntarily revert to Bruce Banner and letting Gen. Ross's Hulkbuster units detain him are two instances of this star-spangled phony's magnificence in bastardry.
Discord from the opening episodes of season 2. It doesn't hurt that he is both apparently inspired by and sharing actors with another magnificent bastard, Q. He's as old as — possibly older than — both Luna and Celestia, and the Avatar of Disharmony that ruled Equestria in an endless maelstrom of anarchy and madness and led to the discovery of the Elements of Harmony; yet he's also one of the Largest Hams available, while still being incredibly sneaky and evil. By the end of the first episode, he's played everyone for fools without even seriously trying, all the while enjoying every second and relishing in the mayhem and suffering he causes. He certainly doesn't fit the part about not being unnecessarily cruel, though, since that basically ishis goal. It's all summed up well in his fan-made Villain Song"Neverending Strife".
He almost does this in "Keep Calm and Flutter On" too, though he ends up getting played by Fluttershy, of all ponies after getting Fluttershy to promise to never use her Element of Kindness against him again, which makes it impossible for the Elements to imprison him in stone. This turned out to be his plan the whole time, banking on Fluttershy to play to her Element of Kindness status and stick up for him despite her friends' insistence that he was playing her. Even after he promises to reform he still has an out, adding in a "most of the time" while making his promise to Princess Celestia.
Queen Chrysalis is a more straightforward example. She shapeshifts into the exact lookalike of Princess Cadence in order to marry then bump off Prince Shining Armor so that she can rule Equestria. She's also an Emotion Eater who possesses the ability to gain power from other people's love. When her true identity is exposed, she reveals her plan: using the power she's gained from Shining Armor's love to defeat Celestia (albeit just barely) and take Equestria by force, making her a Magnificent Bitch who managed to hold the Villain Ball and still survive for slightly longer than usual.
Princess Celestia, has shades of this. She kick starts the plot by giving Twilight orders to make friends with a letter that doesn't mesh well with the received letter, implying that it was prewritten. She sets the Summer Sun Celebration in Ponyville, within walking distance of the Royal Pony Sisters castle containing the Elements of Harmony. She may have know which ponies where in charge of different parts of the preparation and given Twilight the checklist to look into each part, putting each pony in contact. The rest is strictly Wild Mass Guessing territory.
Spider-Man: The Animated Series gives The Kingpin and The Red Skull this treatment. The former is a crimelord who is behind almost every godawful thing that happens in-series, mastermind The Syndicate and the Insidious Six from the shadows, consistently evading incarceration, and frustrating Spider-Man at every turn. The latter's a Nazi spymaster who has backup plans for every situation, anticipates every contingency, and is only taken out via Captain America's Heroic Sacrifice.
Jerry Mouse in Tom and Jerry can be this depending on the situation and how his actions are presented. Other times, he's a Guile Hero.
While The Hacker suffered from Villain Decay, a new villain named Ledge becomes this when he tricks the Cybersquad, and Hackerizes them (minus Inez) and he Hackerizes almost all of the citizens in Sensible Flats,all to impress the Hacker. And, that he succeeded in hurting the Cybersquad more than The Hacker ever did made him a dangerous foe.
XANA wasn't initially much of this, but four seasons of evolution through Jeremy's abuse of the Return to the past made it gradually smarter and more powerful, turning it into a Chessmaster, then a Manipulative Bastard, and eventually going toward Magnificent Bastard territory.
And just how do we know that all those times it caused all those calamities which forced Jeremy to use Return to the past weren't part of a Batman Gambit to make itself more powerful in the first place?
Belphegor, the main antagonist of the "Belphegor" French animated series could qualify as one. He's a Diabolical Mastermind, good at manipulating people and anticipating everything that's thrown at him, so he's never once caught or his identity revealed. You have a trap door in your house that he's conveniently standing over? Well too bad, he knew and had already made it unresponsive to your device! It helps that he has cameras installed almost everywhere in Paris, uses his mooks to spy, steal and kidnap for him (in the few cases he doesn't just do it himself), and apparently has enough money and access to high-tech gadgets and top secret, untested military technology, that can make a mad scientist drool at the thought. To actually make him lose his cool, you have to do something pretty terrible or disruptive to his plans, that could cause a really angry response. Otherwise, everything you do is met either with boredom, slight amusement or mild annoyance on his part.
Ghostfreak falls into this category too. He rode the DNA of another alien into the Omnitrix so that he could manipulate whoever ended up with it into doing his dirty work. It was heavily implied that he was behind the transformations that Ben didn't choose, a large amount of which resulted in Ben turning into . . . well, him; Ben acted meaner whenever he was transformed into him, which means that Ghostfreak was influencing him to some degree. He ended up summoning his minions to Earth while Ben was transformed into him (presumably controlling him entirely, which it was revealed he could do) with a plan to bring him back to life and turn Earth into a world of darkness just so that he could roam the planet without having to wear his outer skin. In the end, it was only his sheer arrogance that got him killed (twice) by exposing himself to sunlight without his outer skin, and the second time he went back into the Omnitrix while leaving his body to die. Oh yeah, and he played Vilgax in Alien Force, taking control of his planet just so he could get another chance to take Ben completely. The only way for him to be permanently destroyed was for the Omnitrix to be destroyed, which Ben did after getting the Ultimatrix.
And let's not forget Aggregor, who managed for his whole story arc to trick the heroes into doing his bidding.
He's finally Out-Gambitted in Season 2, Episode 13, when the gang pulls a Batman Gambit on him and the rest of the original Mystery Incorporated to get them to reveal the location of their pieces of the planeospheric disc, leaving Pericles and his comrades with nothing. However, he ends up rebounding big-time.
The only other Scooby-Doo villain who qualifies is Ben Ravencroft, the charismatic book author descended from a witch from "The Witch's Ghost" movie. He has two things in common with Pericles: his status as this trope, and the fact that his downfall comes from his success in his ultimate goal. Oddly enough, he bears a striking resemblance to David Xanatos. Also, he's voiced by Tim Curry.
Generator Rex gives us Black Knight. From posing as a Reasonable Authority Figure, keeps her own true power hidden to use at later date when necessary, plays politics with the Consortium, and pulling off a success starscream to gain supreme power. She even admits that she wants power, believing that you have to admit it to yourself to get it. Throughout it all, she shows absolute Nerves of Steel, is soft-spoken, polite, acts as a Friendly Enemy despite being a ruthless foe, and so forth. Even when defeated, she ultimately escapes and becomes a Karma Houdini.
Greg Weisman, responsible for the above Magnificent Bastards of W.I.T.C.H., The Spectacular Spider-Man, and Gargoyles, has also produced The Light of Young Justice, a Legion of Doomnote consisting of Vandal Savage, Ra's al Ghul, Lex Luthor, Queen Bee, Ocean Master, the Brain, and Klarion the Witch Boy, with Ocean Master being replaced by Black Manta in Season 2 to erase any conception of the Legion of Doom as campy or incompetent. Unfortunately, some audience reactions indicate they may be too far in the other direction: when every scheme the heroes foil is actually a distraction from The Light's true plan, tension becomes reduced and the initial 'wow, what a twist, what an awesome group of villains' becomes 'sigh, time to watch the heroes waste their time and then not find out what The Light was actually planning, how exciting.' Well, at least until "The Summit", penultimate episode of the second season, in which the Light, while not completely defeated, certainly has their immediate plans blow up in their collective faces (with some help from the heroes), resulting in Black Manta and the Brain being captured, Ra's al Ghul being killed (albeit temporarily), and Vandal Savage and Klarion fleeing the planet aboard War World.
As of Season 2, Nightwing qualifies, having pulled off a massive long-con on the villains and his own allies.
Eric Cartman from South Park has been known to be this on occasions. Despite being an ignorant slob who is shown to have little common sense in many things, he displays an uncanny level of charisma and social savvy. Very often, he is shown to be capable of manipulating hordes of people into going along with his latest audacious plan, whether they are aware of it or not, and treat it like sheer child's play. A few shining examples can be found where he staged the utter ruining of a teenager who scammed him out of sixteen bucks and manipulating Cthulhu itself.
Abraham Kane of Motorcity. He's a Villain with Good Publicity and lots of money, usually able to talk to the Burners through a screen (to make himself appear larger) rather than face to face, which makes him look impressive. The Duke of Detroit is also this at times, although more of a Friendly Enemy. As he's a Large Ham, he often likes to oppose the Burners in style, particularly with lots of lights and music, as well as firing at the Burners with limousines as ammo.
In an episode of Archer, Lana decides to get even on Cyril for cheating on her by having sex with everyone else in the office. At least that's what she tells Cyril. In reality, she makes all the guys pay her for the privilege of saying they had sex with her.
Gillette: [I'm] confused. If you told every guy the same thing, then they all know that none of them had sex with you, so they're all going to realize that they're all lying.
Pam: Hey, yeah!
Random office guy outside door: Wait a minute...
Lana: But remember: They're dudes.
Second random office guy outside door: What?
First random office guy: Uh... I had sex with Lana.
Pavel: We now present the one and only warrior worthy of locking discs with the traitorous Commander Paige... ME!
Pavel is a bush-league Starscream compared to his boss, General Tessler. Legitimately, his tactics should earn him a 0% Approval Rating, but his Affably Evil persona and carefully cultivated bag of half-truths leave Beck as a Hero with Bad Publicity, and earned him the loyalty of Paige even after he slaughtered her friends from the medcenter.