Some of the Gym Leaders and Elite Four members in Pokémon. While most of them (with the exception of Giovanni) are good guys in the games - Lance and Lorelei even helping out the player character at key points - Lt. Surge, Koga, Sabrina, Agatha, Bruno, Lorelei, Lance, Karen, Will and Pryce became villains in the manga adaptation Pokémon Special. To be fair, though, Pryce is a more sympathetic Anti-Villain, Lance is a Well-Intentioned Extremist, and most of the other characters listed reform later on, with the exception of Agatha.
This is utilized to a lesser extent with their anime counterparts. Sabrina is converted into something of a demonic witch who antagonizes Ash and co., while many others, most notably Lt. Surge, Erika, and Skyla, are egotistical Jerkasses with a condescending demeanor towards their challengers (or, in Erika's case, towards those who don't appreciate the perfume her gym makes). All of them make friends with the heroes in the end.
Pokémon Special has a downplayed example with Norman. In the games, Norman is a kind, gentle person who respects his child's wishes and would most likely not use physical violence. In the manga, Norman is a lot meaner and beats up his son for disobeying him. Despite his harshness, he is on the side of good - he is genuinely supportive of Ruby.
In Pokémon Black and White, N is a very sympathetic Anti-Villain with good intentions. He eventually makes a Heel-Face Turn in the sequel games, helping the player against Ghetsis, his much more evil adoptive father. However, in Pokémon Special, N has fewer redeeming qualities and manages to convince White's Tepig to leave her. His goal also seems to be more like Ghetsis' goal than in the games.
In Pokémon Black 2 and White 2, Colress, while still a scientist in the employ of Team Plasma, does encourage the player and even gives them a device needed to progress further in the game. He is involved with Team Plasma For Science! and is not particularly interested in their goals, expressing distaste for Ghetsis. In Pokémon Best Wishes 2 Episode N, Colress is a true Mad Scientist who experiments on Pokémon to the point of torture, uses mind control on the Pokémon in his introductory episode (including those of the main characters), and is more than willing to hurt Ash and his friends to prove his theories. He is also more appreciative of Ghetsis due to Plasma's "providing" increasingly more difficult "subjects" pushing the theories further. Colress in the game has a Heel-Face Turn, willingly disbands Team Plasma, and becomes The Atoner after Ghetsis is defeated, while his anime counterpart is arrested by Looker. The Anime counterpart does come up with the idea for a Pokemon translator, but after he's arrested and in a way emphasising his Blue and Orange Morality.
The Pokémon Special version of Colress is portrayed along the same lines as in the anime.
Gendo Ikari: In the anime, he is Ambiguously Evil, he sincerely praises Shinji for his combat performance at one occasion, and with his Famous Last Words he regrets having been a bad father to him. In the manga adaptation, he is unquestionably evil, has a massiveGod-complex, and outright hates Shinji. In the manga, he's also implied to have personally killed Kaji, whereas it was unknown if he had anything to do with it in the anime, even though he was hinted at being involved somehow. He's somehow even worse in Campus Apocalypse.
In the Mai-HiME manga, the main antagonists of the first arc are Haruka and Yukino, the latter of whom is friends with Mai and Mikoto in the anime, and the otherwise heroic Akira assists them. By contrast, Shizuru never turns Psycho Lesbian, and Nao (reluctantly) helps the heroes after the teams merge.
Wrath and Envy were already horrible monsters in the manga, but the anime made them worse. Wrath (now named Pride) loses all of his Noble Demon qualities and his last scene involves him strangling his Morality Pet, Envy had his sadism cranked to maximum, and both lose their Alas, Poor Villain moments.
In a similar but lesser manner, Shadow the Hedgehog in the Sonic X anime. In the games, Shadow started off a vengeful weapon ready to destroy Earth's population in honor of his murdered friend. Throughout his story however, he is portrayed with a palpable sense of doubt and emotional conflict, before ultimately pulling a full Heel-Face Turn two games later. In the anime, he roughly follows his games counterpart's story, but maintains his more sinister neutral alliance and is The Unfettered to the highest scale (at least once perfectly willing to kill a child in cold blood, along with anyone who defended her, if it meant stopping a Bigger Bad).
Black Widow and Hawkeye are usually depicted in both the 616 and Ultimate universes as Anti-Hero allies of SHIELD. The MovieRise Of The Technovore depicts them as much more antagonistic and villainous.
In the manga of Deadman Wonderland, the staff of the titular prison Hand Wave the prisoner deaths in the dog races by claiming that they are done with special effects. In the anime, the special effects angle is done away with; and the prison openly admits that many of the competitors do not survive and die brutal deaths.
Kaede Fuyou from SHUFFLE!. While not exactly a villainess, she was a sweet and simple Yamato Nadeshiko in the original game... and then she became quite the infamous boxcutter-using Yandere in the anime.
The Dark World Fiends were presented as villains in the third season of Yu-Gi-Oh! GX, which contradicts the flavor text of some of their cards in the game and the Master Guide 2, which claims they are not evil. In fact, the flavor text on Zure, Knight of Dark World's card claims that he "never oppresses the commoners", while that's probably what he's most notorious for doing in the anime.
Also, in the manga version, Jim Cook is an antagonist who is far more malicious than his lighthearted and benign anime counterpart. It's not his fault, however; he's a Brainwashed and Crazy pawn of Tragoedia.
In the manga version of Yu-Gi-Oh! 5Ds, pretty much every character has a different background and personality, but Rua and Ruka more so than any other. They start of as villains in this version (and rather sadistic ones at that) very unlike the kind and innocent children they are in the anime. (There seems to be some strong potential for redemption in the current storyline, however; Ruka is already well on that path.)
In the manga version of Chrono Crusade, Big Bad Aion is portrayed as misguided and possibly insane, but sympathetic, having turned to evil deeds in a desperate attempt to fix what he felt was a corrupted system after learning an Awful Truth. In the anime, he was turned into the literal Anti Christ.
Prétear: In the manga version, one of the Leafe Knights ( Sasame, the Knight of Sound) is strongly hinted to have been in love with the villain in the backstory, but he's definitively a good guy and remains that way for the entire story. In the anime, where Fenrir plays a bigger role, he eventually breaks down and becomes her minion because of his Mad Love.
Queen Beryl of Sailor Moon was a villain in the manga, but an ultimately tragic figure who was manipulated by Metaria into her crimes in her past and current incarnations, and ultimately doomed not by her villainy, but her own belief that she was beyond redemption at this point. In the anime, she's a straight-up evil villain who willingly and loyally serves Metalia.
The first anime of Black Butler does this with Queen Victoria, of all people. In the manga she's a straight Cool Old Lady, while in the anime she's responsible for Ciel's parents' deaths, and planning to start a world war to "cleanse" the world with her angelic accomplice, Ash.