Sucy Manbavaran from Little Witch Academia is the witching world's equivalent of a mad scientist. She loves coming up with new potions and poisons, then testing them out on unsuspecting victims. Mostly her friends. Sucy's Establishing Character Moment is her trapping Akko and Lotte in a net as bait for a cockatrice so that Sucy can steal one of its feathers as an ingredient for her newest potion.
In Valvrave the Liberator, we have Dr. Tokshima, a man responsible for creating what he calls a new life form, "homo sapiens novus", and is completely happy that they are superior to humanity. He laughs constantly, and compares himself to god in a somewhat funny, somewhat disturbing fashion, because its less of a dramatic declaration and more of a question he asks himself logically.
When he boasts about his son, Haruto, to his colleagues, he is holding a picture frame of what seemed to be a picture of Haruto. Except it's not a picture of Haruto in person. It's Haruto's genetic map. Even his colleagues are disturbed by that.
Dr. Hell from Mazinger Z. In some versions (including the original manga), Juzo Kabuto is a mix of this and The Professor. And he has a handsome and Hot-Blooded grandson named Koji Kabuto, the main character.
In Yu-Gi-Oh! 5D's, Akutsu (the scientist who developed the current Momentum generator) was certainly nutty enough to fit the Trope (and he did work for the Big Bad of season one), but he seemed harmless.
Professor Souichi Tomoe from Sailor Moon. In the first anime version he was possessed by a demonic being that lived in his eye; in the manga, he was just plain evil.
Dr. Franken von Vogler from the Giant Robo OVA was introduced as a classic ranting Mad Scientist. The series subverts this trope, as successive flashbacks reveal more about his real motivations.
Icchan from Kidou Tenshi Angelic Layer is often mistaken for a Mad Scientist; he seems to encourage it, making over-the-top dramatic entrances, speaking cryptically about his creations whenever he can, and wearing his lab coat all the time.
However, his invention makes sense, is based on diligent research, operates on the notion that the principles discovered in previous discoveries can lead to new ones, is dependent on capitalism to provide funds and is profitable for mankind in general. Mad Scientists everywhere are very, very disappointed in him.
Mayuri Kurotsuchi is an extreme example, a combination of Mad Scientist, Mad Doctor and Ax-Crazy to boot, openly boasting of the thousands of souls he's experimented on in his studies. Yet he leads one of the Soul Society's 13 squads (his contains lots of quirkyassistants) and is a valued member. You begin to see the problem that the rest of Soul Society has with the administration.
His Arrancar equivalent is Szayel Aporro Grantz, who shares his twisted science, represented the aspect of death known as "madness" and whose own Quirky Miniboss Squad existed solely to provide him with food whenever he needed to heal injuries. In the battle between Szayel and Mayuri, the fight ended up boiling down to which scientist was the most insane and the most capable of using that insanity in disturbingly creative ways. The winner, by a large margin, was Mayuri.
Aizen is one as well. His madness is quieter than Mayuri, harder to see until he's unmasked as the villain early in the story. As the story develops, his madness becomes more and more noticable as the stakes get higher and higher. His shinigami/hollow/human/quincy experiments, however, have never been the experiments of someone with a sound mind, what with the constant killing For Science! and his "I will become God!" obsession.
Somewhat unusually for a Mad Scientist, Aizenlikes when his experiments don't produce what he wanted them to, finding it more interesting when something unexpected happens.
Dragon Ball Z's Dr. Gero built a series of androids, and then turned himself into a cyborg, in order to exact revenge on Goku, who destroyed the Red Ribbon Army decades ago.
Fullmetal Alchemist, instead of dealing with the Mad Scientist, revives its predecessor-trope, the almost forgotten Mad Alchemist (see below).
There's Shou Tucker, who, under the pretense of having to produce good results in order to keep his license as a State Alchemist (although he later admits it was mostly "just to see if I could do it") combines his own young daughter, Nina, and her pet dog into a chimaera, condemning them to a Fate Worse than Death from which Scar is forced to release them via Mercy Kill. He doesn't fit the traditional profile of this trope (he appears quite calm and kind for most of the time we see him), but there is no doubt that he crossed the Moral Event Horizon on that one.
The Movie of the 2003 anime introduces a scientist who is severely ticked at the world's alchemists for making his work worthless. The "mad" part of this shows up when he reveals that he discovered Uranium and threatens the Elrics with a hand-held nuke. Clearly he never tested the thing.
Weiß Kreuz is almost as fond of these as it is of Mad Artists - see particularly Takatori Masafumi, and Tsuji Mayumi in Weiss Kreuz: Glühen.
Hajimete no Aku. The protagonist Jiro is a self-proclaimed Mad Scientist, Although in fact he seems to be incapable of doing anything evil.
The eponymous Dr. Kishiwada of Dr. Kishiwada's Scientific Affection. Clinically insane and more than a little sociopathic.
Ginias Sakhalin from Mobile Suit Gundam: The 08th MS Team, the head of the Apsalus Project, which could be best described as a miniature Death Star that kills cities instead of planets. He starts out relatively sane if overly dedicated, but he deteriorates as time goes on.
Granted his looks are a bit more... delicate and effeminate than this trope usually entails. As in, he looks more like a stereotypical hairdresser than mad scientist.
The Elder in Chrono Crusade is a mild example of this trope. He's not completely insane, but his inventions tend to be quirky at best and downright dangerous at worst. Some of the things he's responsible for in the series include purposefully allowing Rosette to steal an experimental bullet with a demon trapped inside so he wouldn't have to test it himself, and apparently fusing a friend with demonic legion in order to make him a better fighter. Oh, and he's a Dirty Old Man to top it all off.
Nina Einstein from Code Geass, a Teenage Mad Scientist Girl. She is particularly known for being a Psycho Lesbian and inventing weapons of mass destruction.
Earl Lloyd Asplund is an older, slightly more comedic version of the trope. His Bunny-Ears Lawyer status has earned him the Fan Nickname "Lloyd Aspie".
Lloyd plays with the trope as while he is eccentric and disrespectful, he is fully aware that he is a mad scientist. Also, he is the only (non-royal) noble in the series to have no lust for power and not be racist, and in that respect is in some ways the Only Sane Man.
However, Lloyd plays it straighter in the Alternate Universe manga Suzaku of the Counterattack, where he willingly goes along with Prince Schneizel's plan to gain C.C.'s powers in order to (you guessed it) Take Over the World, even though it could potentially destroy the Earth (and almost does, if not for the intervention of the heroes).
Professor Franken Stein of Soul Eater, whose love of dissection is played for laughs early on. The "mad" aspect becomes important later on, as madness is somewhat more concrete in this world.Medusa definitely counts as well. Eibon could count as this as well, in both the anime and manga, because not only does he eradicate the madness of knowledge but he teamed up with Arachniphobia (an evil witch) to invent his magic tools and demon weapons, although it seems as if he has truly benign intentions at heart.
Stein's likening for cutting people up is played for laughs, but it's also what he seriously would have done to Medusa given the chance (and Spirit, and Maka, and Kid, and anyone he saw as interesting..). In the witch's case he settles for dismembering her and shoving a scythe blade into her skull for good measure.
Getter Robo has a few. Saotome is the most famous example, though he's very low-key (except in the Armageddon OVA) about it and fairly normal on the surface. Professor Shikashima on the other hand has several screws loose (and indeed, actually has one lodged in his skull) but his craziness is mostly played for laughs. In Getter Robo? Hayato replaces Saotome as the leading scientist, with his trademark Ax-Crazy streak.
While Shiho Miyano of Detective Conan may not qualify as a Mad Scientist, since she was forced into doing her research, her father Atsushi certainly does. The series specifically mentions that her father was considered a mad scientist even by the standards of the Black Organization. That's pretty mad. Though Agasa says that Atsushi wasn't that crazy, but actually a rather decent guy. Since he is Shiho-aka-Ai's Parental Substitute, lying about this would be just too risky...
One story in The Kindaichi Case Files features the story of a mad scientist who, during WWII, chopped up soldiers and tried to sew the pieces into the ultimate human. It turns out that the real "mad scientist" was a pharmaceutical company that tested experimental drugs on six patients, all of whom died.
The Pokémon anime loves this trope, especially for villains:
Dr. Fuji, the Reluctant Mad Scientist who created Mewtwo for Giovanni in hopes he'd be able to revive his dead daughter
Dr. Zager, another Team Rocket scientist, who assists Jessie and James in Unova and sports a monocle.
Dr. Yung, from Mastermind of Mirage Pokémon, who is revealed to be the titular "mastermind", attempting to take over the world with super-powerful Pokemon holograms
Butler, in the sixth movie, laughed out of Team Magma for a failed attempt to re-create Groudon, who now travels as a circus magician, but tries his experiment again using Jirachi as a power sourceand ends up having it work a little too well.
Zero, the yandere villain of the eleventh movie, an assistant for an aborted project. After being abandoned by his mentor, obsession drives him to take reviving it a bit too far. And by "take it a bit too far" we mean "threatening anyone who stands in his way with poisonous gas or a giant robot".
Inverted with Irie, from Higurashi: When They Cry. While he did do vivisections on people, and does act a bit "odd" toward Satoko, he's an honestly nice, smart father figure.
But played terribly straight with his boss, Miyo Takano, who was perfectly willing to kill the reported host of a Hate Plague to make a village suffer the said plaguejust to prove that her grandfather wasn't mad.
Hayate the Combat Butler: Makimura Shiori seems to think that nursing robots need lots of missiles and rocket boosters. Unfortunately, most of her inventions either blow up or go berserk. In one episode, her boss asks her why all of her projects are complete failures. Her answer? "Um, not enough firepower?"
Love Hina: Kaolla Suu is Crazy Awesome in that she's always gotta build bigger and better mechas based on the flying turtle, Tama-chan. These also explode on a regular basis. She even lampshades it in one episode by saying that having your creations explode spectacularly just seems like something a Mad Scientist would do.
Hollow Fields is a manga about a school for mad scientists' children. The children get a classic education in things like making Steam Punk killer robots, making hideous animal hybrids, poisonmaking, and many, many other subjects.
Dr. Schroeder from Darker Than Black is a nice old man, but, as a review put it, "just when you start thinking he's fairly normal, he goes on a slightly psycho, childish rampage".. He only wants to rid the Earth of the Alien Sky that shut all space programs down. The side effect he expects would be killing as many people as there are stars in the sky. A problem not explored in series is that there's no way to test his project and ensure that in process the whole Earth will not suffer the same fate as all those vanished rockets, turn into one big Gate, etc. He is quite sure his theory will work out exactly as he expects, so What Could Possibly Go Wrong??
Dr. Etou from the Shikkoku no Hana manga, on the other hand, is a grinning, stuttering and almost drooling specimen — when his superior snaps him out of rants by punching this doesn't even look like needless cruelty.
Yoshizumi-sensei of Zombie Loan. He started off as a reasonably sane college scientist, but when Caramelo of the ARRC turned him into a zombie, he snapped. He ends up merging with his "masterwork", the Phalanx, only to be killed by Sawatari.
Hanaukyō Maid Tai. Head maid of the Technology Department Ikuyo Suzuki sometimes becomes one of these. When she does so, her spectacles become Scary Shiny Glasses. In La Verité, her face usually gets distorted as well.
Okabe Rintaro (or HOUOIN KYOUMA! as he sometimes prefers to be called) of Steins;Gate is a self-proclaimed example, often prone to peals of Evil Laughter, bouts of paranoia, and referring to his inner circle of friends as lab members. Yet despite all of this, he can be surprisingly grounded at times, and realizes that he and his friends' dabbling in time travel and poking about a Government Conspiracy could land them in very hot water.
Rinichiro Hagire, the true Big Bad from Deadman Wonderland. He found a way to overwrite people's memories with his own, so that his consciousness could continue to live through another's body, completely under his control. He also started a macabre carnaval in his search for the strongest Deadman for his next "generation." Death was expected by the loser. At the time of the Wretched Egg's birth, he was testing human immunity, searching for a way to improve it, and eventually created the Deadman; he is now trying to turn of the MGS so that the Egg/Shiro can be at FULL POWER, which caused a huge earthquake when she first awoke, submerging the entire city of Tokyo.
Doc from Texhnolyze, who doubles as a Hot Scientist. Putting aside her prosthetic limb fetish and her tendency to have sex with her patients, she also puts wheels on a rat for no reason other than her own apparent amusement.
Dr. Hogback from One Piece, who builds zombies for his master Gekko Moriah, and has no respect for life despite being a doctor.
From the Punk Hazard arc, we have Caesar Clown, who's an even bigger asshole, and even more nuts (Watch out, loads of spoilers ahead). He kidnapped and experienced on children, and used a very dangerous drug on them to keep them from escaping, he has absolutely zero respect for anyone, his forte is weapons of mass destruction, he acts like a nice guy to his underlings only to perform more experiments on them later, he caused an incident that made Punk Hazard into a wasteland, then collected the leftover poisonous gas from that incident to make a Blob Monster, which he later changed back into an even deadlier gas that petrifies its victims... What makes it even worse is that a mole in the Marines covers up all of his actions, allowing him to do as he pleases.
Ivan Alexandr in Marginal. He is obsessed with the womb and runs away to Earth so that he can freely experiment with creating hermaphrodites.
Izaya Orihara of Durarara!! is what happens when a mad scientist tries his hand at sociology. Note that this ends up being impossible to distinguish from a troll.
Mobile Suit Gundam has a rather tragic example with Tem Ray, Amuro's father. Originally he was a decent man (if very distant to his son), but when their home colony is attacked he gets pulled into space and suffers brain damage due to oxygen deprivation. The next time Amuro sees him, he's in a basement cobbling gobbling electronics into "upgrades" for the Gundam and rambling to himself.
Hange Zoe of Attack on Titan is a heroic example, being the eccentric head of Titan research for the Survey Corps. Hange has some aspirations towards being a Fluffy Tamer, but is also responsible for a good percentage of what humanity knows about Titans. Traps, zany experiments involving Eren performing tasks in titan form, and generally terrifying bystanders is business as usual.
Hakase Saotomi and Chao Lingshen from Mahou Sensei Negima!, refer to themselves as having sold their souls to science.
Adam from Mother Keeper is stated to be this by Jim and Zelik. It's yet to be revealed how he earned this title but he did turn a blood-loving terrorist into a superpowered immortal cyborg.
With A Certain Magical Index being staged in a city technologically ahead of the rest of the world by 30 years, it's no surprise there would be mad scientists. One of the most prominent is an entire clan of mad scientists called the Kiharas, and it's strongly implied in the series that all the experiments they get involved in are solely For Science!! regardless of implications. To mention just a few:
Kihara Amata raised and influenced Accelerator from a young age, and even trained him in his vector manipulation abilities. As a result, when Accelerator has to confront him later, Amata perfected his combat so precisely he can reverse the force of his fists once they reach Accelerator's reflection, forcing them past his barrier and hitting him. And Amata isn't even an esper.
Kihara Gensei is the head of the entire clan. Just some of of the things we know about him is that he tricked Mikoto into giving him her DNA map, which set off a series of experiments that resulted in mass-producing clones of her in an attempt to increase the amount of Level 5's. When that proved ineffective, he set off the Sisters project - having Accelerator slaughter the clones in order to reach Level 6. When that gets botched by Touma, he later hijacks the clone Network and forces Mikoto to evolve towards Level 6, knowing fully well that she would self-destruct and destroy all of Academy City if she reached that point. Yes... this man wanted the entire city to burn just to see what would happen.
It is mentioned that the reason Academy City maintains a tight leash over the espers and technology is partly an effort to keep all the Kiharas in one place where technology was at its finest. Otherwise they would spread chaos on a global scale.
New Testament Volume 7 gives us a non-Kihara example in Yakumi Hisako, one of Academy City's Board of Directors. She starts the Agitate Halation project to get rid of all aspiring heroes in the city by tricking them into killing each other. In the process, she gets eaten by her own man-eating roaches, but this all turned out to be a front, as her true objective from the entire chaos was to become an AIM being. Even if she knew her consciousness would disperse within seconds of what she would witness. For Science!! indeed.
Dr. Akihiro Kanou from Tokyo Ghoul. When confronted about intentionally turning Ken Kaneki into a Half-Human Hybrid, he makes a speech about being Above Good and Evil. His experiments have left dozens of innocent people either mutated into mentally disabled freaks of nature or dead, with only four known successes. In response, Kaneki calls him a fucking lunatic.
In Kirby: Right Back at Ya!, one of the many Monsters of the Week is a crazy scientist named Dr. Moro, inspired by The Island of Doctor Moreau (no kidding) who messes with the DNA of Kirby, his friends, the Cappies, and of course, King Dedede and Escargoon, and uses them to create dinosaur monsters that chase after them all throughout Dedede's theme park. His most powerful dinosaur monster was created from Kirby's superior Star Warrior DNA, and he turns really freaky when he's ordering his minions to attack. And to top it off, he has the typical Evil Laugh of any other Mad Scientist.
One of the villains in Hugtto! Pretty Cure, Dr. Traum, is one of these. He doesn't seem to be entirely mad, but he is one of the villains, so he definetly qualifies. Most of his science seems to be related to robots- fittingly, it is later revealed that was the one who made Robot Girl Ruru, who had undergone a HeelFace Turn at the time of his debut.