Complete Monster/Pokémon Anime

Though Pokémon is a children's series, it isn't free of this trope - not in the original video games, nor in their various adaptations.

The Pokémon anime is mostly Lighter and Softer, with the worst of its antagonists being more jerkasses as opposed to completely evil - to a lesser extent, this applies to the various Pokémon manga media.

Rarer but still present are these notorious individuals, who even this series can't completely gloss over:

Pokémon Anime

 * Pokémon Hunter J from Diamond and Pearl. As her title implies, she hunts rare Pokemon to sell on the black market, and has no qualms with stealing them from other trainers. She is willing to go to any length in order to capture these Pokemon for her clients, including attempted murder on her fellow humans. In her first appearance, she drops a section of her airship containing several of her own men, and the Pokemon that she’d stolen, just in order to be rid of our 10-year-old protagonist, who was in the same section of the ship. She shows absolutely no hesitation or remorse for this action, and Ash had only been a slight inconvenience to her at that point. In her follow-up appearances, she continued to demonstrate her sociopathic, greedy, ruthless nature, as well as her total disregard for any form of life by continuing to steal rare Pokemon, setting fire to a large section of densely populated forest in order to kill Ash, ordering her Salamance to attack humans directly, commanding her Drapion to squeeze the life out of Ash, and abandoning one of her clients to the police the second after she got paid. In her last appearance, she's willing to do a job for Team Galactic, who is planning on wiping out the universe, all for the sake of lining her own pockets. In the 800+ episodes of the Pokemon anime, she’s the only character who has proven to be purely evil with no redeeming qualities. Because of this, J winds up being one of the few anime characters to actually die, having her flying vehicle destroyed and sink to the bottom of a lake with her still inside.
 * Actually averted with Ghetsis in Best Wishes, whose worst actions are entirely implied. For all his screen time, he's pretty standard as far as Big Bad Evil Overlord villains go.

Pokémon Films

 * Vicious AKA The Iron Mask Marauder from the fourth movie is a punk bruiser with no remorse and a sadistic streak a mile long. In his first scene, he tortures and perhaps even murders an elderly former Pokémon poacher after forcing information out of him. He brainwashes all his Pokémon, including forest legendary Celebi, which he uses to go on a rampage in said forest, attempting to destroy it as a show of power. He has no qualms with physically harming and possibly even killing kids like Ash and young Sammy Oak. And he uses Jessie as an audience for the reveal of his plans--to eliminate Giovanni and take over Team Rocket to conquer the world himself. That's right...the implication is that this guy's worse news than Giovanni! Vicious is also notable as using the first instance of what would later be called Shadow Pokémon.
 * The worst of all in the anime universe is Grings Kodai, the antagonist of Pokémon Zoroark Master of Illusions. He kidnapped mother and child Pokémon from their homeland, imported them into another region, and blackmailed the mother into doing his bidding by threatening to kill the child. All of this is to cause the evacuation of a large city so he can find an energy cluster left behind by time-traveling Pokémon Celebi and absorb it, renewing his ability to see the future, which he aquired twenty years prior at the cost of annihilating the city's plant life. He's willing to destroy the city's ecosystem a second time, and why is he willing to do this? He's a wealthy and powerful businessman - he's doing it for the money.
 * He's got even worse traits than that. He forces Zoroark to allow him to obtain the Time Ripple by electrocuting her child right in front of her to the point that Zorua actually says he thinks he's going to die! Then, to make things worse, Kodai has his Pokémon try to kill Zoroark, since he's got Zorua in the palm of his hand and Zoroark is defenseless so long as he does, this means he does this for no reason except he CAN. He even goes so far as to say that he enjoyed doing it! And he manages to one up himself by trying to murder Zorua and Zoroark in cold blood when they trick him, despite the fact that he could've just went on ahead and ignored them to absorb the Time Ripple or flee (the latter of which Vicious and Pokémon Hunter J attempted when they were stopped). And he actually succeeded in killing Zoroark - though Celebi saved her, it doesn't change the fact that Kodai committed, thus far, the only successful cold-blooded murder of a Pokémon (all other times were accidental or just a side effect of what the villain was doing, but Kodai killed Zoroark intentionally, directly in front of the child she was in the middle of being reunited with!)}}. With all that said, his Humiliation Conga (or Karmic Death, if you're going by the manga) is immensely satisfiying.

Pokémon Special

 * Most likely Sird, a member of the Beast Trio from the FireRed and LeafGreen arc, who, unlike her comrades, is shown to commit atrocities For the Evulz and - if her latter appearances are any indication - is a Hidden Agenda Villain with probable Chronic Backstabbing Disorder. According to Riley, her aura is one of pure malevolence and evil. Even Cyrus, himself an Omnicidal Maniac, pales in comparison to her.
 * The Masked Man from the G/S/C arc seems to qualify, but this is majorly averted in the end where we find out that he is an Anti-Villain and his motivation is to reunite Lapras with its parents, and he actually cared for the children he kidnapped but due to fact that his heart was "frozen over" could not express it, and he is just an insane but lonely and miserable old man.
 * Here comes Ghetsis in the Unova arc! And seeing as Pokémon Special is Darker and Edgier than the games and N, while still an Anti-Villain, is a bigger jerk in this manga than in the games, Ghetsis here might actually be worse than his game counterpart due to how Faux Affably Evil he is while committing his atrocities. He keeps the demeanor of a kindly, benevolent minister the whole way through, even as he's having his Eelectross electrocute Black into paralysis, overpowering and capturing Gym Leaders, torturing them, and hanging them up on crucifixes, threatening the life of an innocent hostage to force the one resilient Gym Leader into surrender, admitting that he purposefully warped his own son, whom he has never loved, to suit his selfish plans, and attempting to kill Black in order to keep him silent by sending out a team of Pokemon specifically trained to counter Black's team so that they cannot protect him! He even indicates he'd kill Black's Pokemon too! And then even after he's been defeated, he manages one extra act of cruelty by using his associate's Pokemon to knock Black towards Reshiram, who was currently reverting back to it's dormant state, so that Black ends up sealed inside the Light Stone as well, and Ghetsis uses Black and White's distress as an opportunity to make his escape, mockingly stating that it's been fun but he hopes to never see Black's face again. His polite ways contrasting with his heinous deeds is reminiscent of Freeza. And as of the current arc, he's yet to get his comeuppance.

Pokémon: Diamond and Pearl Adventure

 * Charon was a money-obsessed Jerkass in the Pokémon games. But his method of introducing himself in Pokémon Diamond and Pearl Adventure is to order his agents to suicide bomb a crowded stadium. Of course, it fails, but his intent is clear. He holds no regard for the lives of others and plans to control the world with money made from selling legendary Pokémon. Two of his organization's top officers leave to find the previous leader--Charon tries to kill them. Which becomes even worse when you find out that said previous leader is being held captive in Charon's base. And as a capper, that previous leader, who goes on to rally the remaining agents against Charon, had previously tried to destroy the UNIVERSE.
 * He also does nasty experiments on Pokémon that essentially turn them into Shadow Pokémon, meaning that where the games version of Charon has Team Rocket's mindset, DPA!Charon is every bit as evil as Cipher.