In a similar vein, the manga turns Jack the Ripper into Grell (a clumsy butler who is actually a sadistic chainsaw-weilding Shinigami) and Madame Red (the protagonist Ciel's aunt and an abortion doctor, who was angry that her victims could get preganant when they didn't want children and thus chose to get abortions, when she herself wished to get pregnant and could not).
The first season of the anime does this to Queen Victoria, of all people, who sides with Angela/Ash the angel in an attempt to "cleanse" the world of sin with the implication that she sided with him/her after her husband Prince Albert died and it unhinged her. She's a straight Cool Old Lady in the manga, however.
Le Chevalier d'Eon turned several real-life historical figures (including the title character) into heroes and villains of a life and death struggle for control of the world. The Big Bad of the series ultimately turned out to be King Louis XV.
Benjamin Franklin betrayed the American Revolutionary movement after being bribed with titles of nobility. This led to a British ambush where George Washington was murdered and the American Revolution was crushed into fine dust.
In Drifters, the so-called Drifters are dead heroes from our world. They are sent to other worlds to battle the Offscourings - also heroes from our world, but decidedly anti-humanity. Amongst the Offscourings are people like Jeanne d'Arc (a Pyro Maniac) and Anastasia Romanova (An Ice Person). It's implied that Drifters are generally less-than-stellar paragons of humanity who died as they lived (Oda Nobunaga is a drifter), while Offscourings are people who were noble and good in real life but died unjustly (explaining why they've obtained a violent hatred of humans). The leader of the Offscourings is implied to be Jesus.
JoJo's Bizarre Adventure Part 1 turns Jack the Ripper into a vampire working for the Big Bad, Dio Brando. It also explains why he disappeared, The main character, Johnathan Joestar disintegrated him. To top it all off, he fights by shooting scalpels embedded in his muscles!
One Piece has many characters named after real pirates. Blackbeard for example is similar to... Blackbeard, except that One Piece's Blackbeard has the abilities of unholy darkness and earthquakes that can sink entire islands, and he is being set up as the most probable Big Bad of the entire series.
Pretty much all of the villains in Read or Die are this where they are given weapons based on what they created. Though they are actually clones of said historical people.
The Rose of Versailles turned some historical figures (like Madame du Barry and specially both the Countess of Polignac and the Duke of Orleans) into series antagonists, which result in some God-awful moments for people who actually know a thing or two about those characters. i.e., the real Countess of Polignac was extravagant to the max and apparently more than a little cold and calculating, but nowhere near the levels she gets in the show, and the Duke of Orléans wasn't exactly a peach either but he wasn't as much of a Smug Snake as the series shows.
Souten Kouro's Zhang Rang, leader of the 10 eunuchs. He manages to rape Shui Jing despite not having the necessary instrument.
In Vinland Saga, the Danish chief Thorkell the Tall, who was one of the commanders in the occupation of England, is turned into a larger than life Blood KnightPsycho for Hire who will work for almost everyone when it promises to get him into lots of brutal battles.
Naruto has the Fourth Kazekage, who we only meet after his death and mostly showed up in flashbacks of the son he abused. By the time he actually showed up for readers to objectively see, he'd been solidly in the villain category for years. Turns out her was more along the lines of an extremely pragmatic ruler who faced a lot of sadistic choices in his life. Though most generally agree that his decision to force Gaara's caretaker to tell him that he hated him and that he was and never would be loved after attacking him in order to measure his worth was just downright stupid, which he later on came to acknowledge.
Madara Uchiha was primarily remembered in Konoha for betraying and fighting the first Hokage and summoning the Kyuubi out of jealousy, with his sole monument dedicated to that battle. The truth ended up being a lot more complex. His reputation was even worse in other nations, and the current Tsuchikage of Iwa remembers him as a war criminal (though that reputation may have been more justified).
Kakashi's father Sakumo Hatake was disgraced for botching a mission in order to save his comrades. A young Kakashi was seriously shocked when his peer Obito Uchiha admitted to admiring Sakumo's actions, and it's implied Kakashi had always pushed himself so hard to make up for his father's disgrace.
Intentionally done by Itachi Uchiha who wanted to be the villain so his brother could be the hero. However lately the truth's been starting to come out in-universe as well.
Tsubasa -RESERVoir CHRoNiCLE-. Princess Emeraude of the Country of Jade is remembered as a fiend who kidnapped children by luring them away to her castle with the power of one of Sakura's feathers, and the townsfolk believe her ghost is at it again when local children start going missing. In reality, Emeraude was a Friend to All Children who had used the feather's power to set up her castle as a safe haven for them during a time of plague. When Syaoran and the others set off to continue their journey, they leave behind proof of their discovery and ask the townsfolk to start spreading the real story of Princess Emeraude.