Most of the adult characters from Neon Genesis Evangelion have doctorates in something. Examples such as Kozo Fuyutsuki (Gendo Ikari's Yes-Man (but with his own reasons), Yui Ikari (The Chessmaster, according to some readings), Ritsuko Akagi ('cause committing mass 2nd degree murder the dummy system is a sane act) and Naoko Akagi (just pure crazy, up to and including murdering Rei I for calling her a "hag"). And all of them are pricks in one way or another. Hey, it is Evangelion after all...
The Doctor from Black Cat. Evil. Although technically his superpower is healing (e.g. reattaching limbs), he's much more interested in the pursuit of knowledge, to the point where he's perfectly happy to conduct human experiments and attempt to vivisect a little girl.
The Doctor is freaking insane when Yusuke fights him. He kills at least 10 people, slices open one of the good guys' spines, slashes another one's stomach, and is generally evil. He also controls his body chemistry so that he can stay conscious the entire time while he's unleashing killer bugs. And releases endorphins so he feels good as his arm is getting shot off. He eventually is knocked out/dies briefly, but is brought back by Genkai.
Because although he was extremely evil, Yusuke at this point in his moral development can't handle killing a human, although killing demons has never provoked his conscience in the least. (Later on after his genes activate and he's a demon, he offers to go find his ancestor Raizen some people to eat because he doesn't want the old guy to die, so apparently he gets over this.)
Doctor never actually does a formal Heel-Face Turn, he just gets off Sensui's psycho train and disappears into the world with a new face courtesy of his plastic surgery skills, chuckling. Later, it is mentioned in the voiceover narration that he opened a dojo dedicated to psychic surgery.
Doctor Muraki from Yami No Matsuei who we are assured IS a real doctor and we do occasionally see doing doctor-type things ... when he isn't committing murder, rape and tormenting the main characters...
One of the doctor-like things he does is run a black-market organ-trading ring on a cruise liner. Another is encourage the cloning research of a protégé of his grandfather's...by killing women and cutting off locks of their hair for samples.
Dr. Nii Jianyi from Saiyuki: so very, very evil. The lead scientist working for Gyokuman Koushou, He's activly trying to resurect Gyumao, an action that will likely bring about the end-of-days, because he's bored. Plus, as it turns out, He's actually a Sanzo, with the power to negate existance. He's also responsible for some of the major evils in the series, such as Brainwashed Kougaiji and Kami-Sama to name a few, particularly creepy, examples.
The Doctor, aka William Conrad, from Trigun. Evil, although reluctantly so.
The Doktor (sic) from Hellsing: Evil. Part of a (Neo-)Nazi organisation, makes vampires and all that fun stuff. To complete the evil combo he also has a sixth finger. (you only notice it if you put attention in his hands as this is never mentioned in the manga)
Doctor Gero of Dragon Ball Z. Evil. His degree is likely in the field of engineering, and he is acknowledged as a truly brilliant scientist, if only he'd stop making evil androids.
GT's Dr. Myuu. Definitely evil, created the parasitic Baby. Later, teamed up with Gero to concoct an evil plan that allowed Hell to invade Earth.
On the good side, we've got Bulma's father Dr. Briefs, who is mildly eccentric (he delays an interstellar manned space journey for weeks to install a cappuccino machine in the craft) but generally helpful.
One Piece: Doctor Vegapunk. Not introduced yet, but his reputations far precedes him; presumably evil, and certainly eccentric. Invented a process that lets inanimate objects swallow fruit.
Scythe Master from Phantom of Inferno is eventually revealed to have a doctorate in psychology. It explains how he was able to erase Ellen and Reiji's memories, and brainwash the Zahlenschwestern into being, though it's subverted because he doesn't use the title of "Doctor".
Black Butler has a doctor in the manga who seems relatively normal and kind. He made prosthetic limbs for circus performers who had lived on the streets before being rescued by Baron Kelvin. Nice, right? Sure, until we learn that those wonderfully crafted prosthetic limbs were made from bones. Bones of children that were captured and kept in cages until more bones were needed. When Ciel learned this he was NOT happy.
Fullmetal Alchemist has quite a few doctors since alchemy is a field of study as well as a practical military strength. Most of these doctors were working for the shadow government to create Philosopher's Stones using prisoners of war...but special mention goes to Gold-Toothed Doctor, the man responsible for the creation of Wrath, the implanting process for which took the lives of around 11 test subjects.
Shou Tucker, who made his own wife into a talking chimera to get his State Alchemist license, and made his daughter into one to keep it. In the manga omakes, he is the only character to end up going to Hell.
Franken Fran: She isn't so much morally ambiguous as much as she is determined to keep you alive through ANY means. Borderlines on this when she's feeling spiteful of someone who wronged her. She even takes requests!
The manga EDD or Eliminate Dangerous Doctors is this. It involves an organization whose sole purpose is to rid Morally Ambiguous Doctorates through "questionable" means (and by questionable I mean outright illegal, including murder, invasion of privacy and espionage).
In Cage of Eden, the closest thing the series has to a Big Bad is the doctor who holds the Pyramid group in thrall with a combination of threats and psychological tricks. He gained power in the first place by spreading a disease, and then only giving the cure to those who swore loyalty to him. Except for the previous leader and said leader's daughter. Those he watched die. And it turns out he isn't even a real doctor.
Dr Slump: the titular doctor, Senbei Norimaki, not only has created Arale, but also creates lots of strange inventions which usually backfire in some funny way. Then, you have his enemy, Dr. Mashirito, who focuses on creating robots strangely named Caramel Men.
At best, while he's certainly done enough original work to deserve several doctorates, he's got a degree from the University of Latveria after he took over the country. Remember, he was disfigured when still a student at "State U." and expelled for causing the explosion. Oddly enough, he goes by doctor, while the legitimately multi-doctorate-degreed Reed Richards goes by mister in his super-id.
And then there's Doom's lesser-known cousin, Doctor Bob Doom, DDS, a one-shot She-Hulk villain.
Batman: Doctor Hugo Strange: Sane enough to hold a doctorate in psychiatry; too insane to perform surgery. (Monstrous enough to try anyway).
Before becoming Scarecrow, Jonathan Crane held a doctorate in psychology.
Doctor Light: Two of them in The DCU, the male one (who also uses his surname as his moniker - Arthur Light) is evil, the female one is good (but very abrasive). It helps that the female Dr. Light happens to be a practicing medical doctor as well as an all-around scientist.
Doctor Poison, Doctor Cyber, and (with what is probably the best super-villain name ever) Doctor Psycho: Evil. According to the Batman: The Brave and the Bold tie-in comic, Doctor Cyber has multiple PhDs in literature.
Doctor Phosphorus: Evil... albeit with some justification.
The Doctor, from The Authority: Good, if often stoned and quite weird. Though able and willing to do some really nasty stuff in the name of good. Taking a country and freezing it briefly in time so it and all its inhabitants end up frozen and exploded in space, anyone?
Several characters in the Wild Storm universe (where Authority takes place) have held the title of "The Doctor," but only the so-called "renegade" Doctor was explicitly said to be an actual doctor, being a heart surgeon. And, ironically, evil. The one given above was a (former) multi-media/dotcom billionaire and his successor was a Palestinian suicide bomber before getting his powers (also good).
The DCU: Dr. Quinzell, Dr. Isley, Dr. Crane and Dr. Elliot? note (Harley Quinn, Poison Ivy, Scarecrow and Hush repectively)
Those may actually qualify as an aversion. While they ARE Doctors, their villainous names don't contain the title.
That aversion also applies to King Tut AKA The Pharoah. He is also a professor and most likely a Ph.D., but Doctor isn't part of his villainous name, either.
Blake and Mortimer: Dr. Voronov: Evil, wants to use a virus in order to wipe out world-leaders. Doesn't hesitate to use children as part of his schemes.
Dr. Niles Caulder, AKA, the Chief. Technically a hero, but caused the disasters that made the Doom Patrol metahumans and made them superheroes just to study them. He also tries to keep them in line through emotional manipulation and the most likely empty promise of making them normal again.
Doc Magnus, creator of the Metal Men. Good, although he spent a Dork Age brainwashed into a would-be world conqueror.
Dr. Mid-Nite from the DCU is a (super)heroic physician. An aversion, since he's definitely Good and not even a jerk.
Doctor Fate from the DCU has a complicated history. He's Good in a cosmic sense, but this may or may not translate to giving much of a damn about humanity (especially in the versions where Doctor Fate is actually being possessed by a Lord of Order as opposed to simply being a person in a costume), and in most incarnations doesn't actually hold an earned doctorate anyway.
A rather humorous example: Howard the Duck's foe Dr. Bong was a Mad Scientist and not a real doctor, but years after his conflict with Howard, he tried to earn a legitimate PHD in psychology. Unfortunately, his first patient during his internship was Deadpool, and suffice to say, that kind of messed things up...
Dr. Mabuse, from a number of German films beginning with Dr. Mabuse, the Gambler in 1922. Not only is he one of the original criminal masterminds, but he also uses "telepathic hypnosis" to force others to do his will. What's his ultimate goal? To spread as much fear and terror as possible and destroy the world, then rule it. Yikes. Luckily, his own self-destructive tendencies ("M'abuse" is French for "I abuse myself") make him his own worst enemy.
Planet of the Apes: Dr. Zaius: Ethically questionable... OK, very unethical. In fact, an antagonist.
Vincent Price from Vincent Price of Dr. Goldfoot and the Bikini Machine: fairly evil.
Very common in David Cronenberg's films, although there's rarely a pure-good or pure-evil doctor.
The Fly: Dr. Seth Brundle is really sweet. Brundlefly, however, is not.
Rabid: Dr. Dan Keloid is okay, until he turns into a zombie.
Shivers: Dr. Emil Hobbes is crazy. Dr. Roger St. Luc is okay, until he turns into a rape zombie. Yes, you read that right. Shivers is a screwed-up movie.
The Human Centipede: Dr. Heiter: A man with a vision. A vision that humanity cannot accept in any means, for good reason.
Species has a whole team of these guys, who while not the villains of the film, have rather unsound ethics. However, only two, Dr Stephen Arden and Dr Laura Baker, actually have doctorates.
Splice has two scientists that are similar to those in Species, namely becoming gradually more obsessed with their creation to the point of throwing ethical considerations out of the window and having sex with it.
Nick: He's been researching tobacco for thirty years and hasn't found any conclusive evidence linking cigarettes and cancer. This guy's a genius. The man could disprove gravity.
Perhaps Doc Brown from Back to the Future escapes this trope because he's not known as "Dr. Brown."
Transformers: The Doctor. "Ve must hav ze brain on ze table! Chop-chop!" Even his little assistant-bots are designed so that he takes the data they've collected by impaling them to death (a rather inefficient use of resources, you'd think.) When asked what his doctorate is in, he has a tendency to reply with something like 'everything'.
House of 1000 Corpses's Dr. Satan. Evil through and through, but he is arguably the best-named doctor of all time.
The main villain of the film Amen is credited only as The Doctor, and is a member of the SS supervising the extermination camps.
A very subtle example in Joe Versus The Volcano. In the beginning, the protagonist is told by an apparently well-meaning doctor named Dr. Ellison that he has six months to live, due to an incurable condition called a "brain cloud". This is what inspires Joe to accept Graynamore's offer to volunteer for a Human Sacrifice for the natives he wants to make a deal with. It isn't until the final scene of the movie that Patricia tells him that Ellison is actually Graynamore's personal physician, meaning he's was likely lying to set Joe up, making Ellison an immoral violator of the Hippocratic Oath.
Victor Frankenstein is a college dropout in the original book. The title is only given to him in later adaptations (as is the title Baron - his family do not hold a barony, and if they did then the title would belong to his father).
In the sequels by Dean Koontz, Victor is indeed a doctor. Also, evil. Also, insane.
The Scarlet Letter has Roger Chillingworth, the inquisitive and respected physician, uses his knowledge of medicine and people to manipulate Reverend Dimmesdale on several occasions to satisfy his own personal paranoia and nosy desires. Made more disturbing when he's shown to be getting an obvious pleasure from watching his patient and implied personal friend squirm at his instigation.
The Doctor (name not revealed), the illegally-practicing therapist from John Barth's novel The End of the Road: highly intelligent, sometimes very perceptive, but amoral, egotistical, and doesn't seem to be doing any good for his patients. Accidentally kills one of the main characters by performing an abortion, which he botches.
The Lord of the Rings: Saruman fits the trope. His "profession" seems to fit the scientist trope in many respects. He does "research" on the rings, and makes a classical faustian slide into the realm of Evil.
Dr Fu Manchu from the novels by Sax Rohmer, "with all the cruel cunning of an entire Eastern race, accumulated in one giant intellect, with all the resources of science past and present, with all the resources, if you will, of a wealthy government...the Yellow Peril incarnate in one man."
Kind of an overarching trope in Genteel Interbellum Setting mysteries, especially those by Christie herself, wherein doctors are very frequently murderers. Several books reference the Crippen case and other murderous doctors who were in the public consciousness at the time. Additionally, doctors had access to large amounts of barbiturates, giving them the perceived ability to murder by drug overdose and get away with it.
Dr. Grimesby Roylott, from the Sherlock Holmes story "The Adventure of the Speckled Band." Attempts to use a snake to kill his twin stepdaughters for their inheritance money, succeeding the first time; however, with a little help from Holmes, the snake turns on him before he can succeed again.
Green-SkyTrilogy: Dr. (D'ol) Wissen was definitely stated to have his hand in some...unpleasant matters, and implied to have his hand in many more including ordering the murder of his research partner Dr. Neshom.
In the afterword of her novel, Evil Genius, Catherine Jinks said that she got the idea from watching her son playing with figurines of "Action Man" and "Dr. X," which got her wondering where and how supervillains get their degrees.
The titular island-owner of Dr Franklins Island is as amoral as they come - hybridizing animals with human genes, refusing to euthanize the ones that survive the process even if they do so in "very twisted forms", incorporating teenaged human castaways into the project and having them turned into monsters, and playing psychological games all the while. His assistant Doctor Skinner, is... willing to go along with most of it (though he's shaken when he speaks to a rayfish that was once a girl) but can't stand the psychological torment, and alternates ineffectual attempts to help the teens escape with working for his boss as usual.
Doctor T in Imminent Danger And How To Fly Straight Into It is an alien version of this. He purchases the heroine and her best friend to use as test subjects. On his first day with them, he removes the heroine's brain. Things only get worse from there.
Smallville was the king of this trope. The wiki actually had a page on evil doctors! Metropolis University must be the world's leading college for obtaining a Morally Ambiguous Doctorate, because almost every single doctor appearing on the show is either evil or a Well-Intentioned Extremist doing unethical experiments For Science! (or, y'know, in return for Luthor money). Even a regular medical doctor Helen Bryce turned out to be evil in Season 3.
Buffy the Vampire Slayer: Doctor Walsh slid from good to misguided to evil in short order before "being skewered by her own Frankenstein-like creation."
Although he is probably not a true doctor, Doc may be an example.
Also there was a season 6 villain called "The Doctor" who dealt in transporting violent demons. It turned out to Spike.
Angel's examples run the gamut from fantastical to the creepily mundane, such as Dr. Meltzer, an eye surgeon with animatronic limbs who stalks one of his patients.
Though he only appears in one scene, a "Dr. Gregson" is responsible for surgically removing the heart from James in "Heartthrob". This renders James (a vampire who is bent on avenging his lost love) impervious to stake attacks. Gregson uses his medical practice as a cover for his species' custom of collecting rare organs.
By and large, trusting anyone with a labcoat in Wolfram & Hart is...not a good idea.
Doctor Who: The Doctor: Though good, Trial of a Time Lord: The Ultimate Foe reveals that he has the potential to become one of the most evil beings in the universe.
Also, exactly what the Doctor got his doctorate in is never stated. Some of the earlier episodes seem to indicate that he most likely did not get his degree in medicine (save for a "purely honorary" degree from working under Dr. Lister [of Listerine fame]), but in law. As an interesting side note, the word "Valeyard" (the name of the Doctor's prosecutor and potential dark side) means "a doctor of law."
Mirror Universe Phlox in the Star Trek: Enterprise episode "In a Mirror, Darkly" where Phlox's role on the ship is still the same, but is now a (still odd and gleeful) sadistic expert of medicinal torture.
The EMH on the Equinox on Star Trek: Voyager. Since they removed his "ethical subroutines" he's psychopathic. Also, when they removed Voyager's Doctor's ethical subroutines, he was ready to gleefully remove Seven of Nine's brain. This wouldn't be so bad, but he has a crush on her.
Doctor Mohinder Suresh of Heroes. A true blue good guy in the first season; evil tendencies started to creep in around the same time he started taking levels in badass in the second season. A screwed-up recipe for homemade Applied Phlebotinum resulted in something a Face-Heel Turn, though. At present, the jury is out on whether he's good or evil.
Dr. House: Good, but only because he sees deathly ill patients as big puzzles and can't resist "solving" them: saving lives is viewed as collateral damage; he doesn't bat an eye no matter how bleak the prognosis is. Many of his actions when in the process of treating a patient are incredibly unethical, dangerous, unnecessary, or all of the above, and he makes all his choices based on his own selfish whims, but his seemingly evil actions almost invariably lead to a lifesaving cure for someone who would otherwise have been royally screwed.
Borderline-parodied in Sabrina the Teenage Witch "Sabrina the Teenage Writer," with Sabrina's poorly written Bond villain "Dr. Bad."
UFO. The vaguely sinister Dr. Doug Jackson appears to fill a number of roles in SHADO, ranging from psychiatrist and medical doctor to prosecuting officer. In one episode Commander Straker calls him "the eyes of the International Astrophysical Committee" implying that Dr. Jackson's role is to spy on him for his superiors (which would explain his wide-ranging brief). This is only enhanced by his noticeable Eastern European accent, which would automatically make the 1970's audience think of Cold WarEspionage Tropes.
LOST has Dr. Juliet Burke (initially on the side of the Others, who have the dubious claim of "the good guys"), Dr. Ethan Rom (seems to have been evil, also part of the aforementioned Others).
Fringe: Dr. Bishop, a mad scientist who specializes in bizarre "fringe science" written off by the rest of the scientific community. Probably Lawful Neutral as he seems to be a member of at least one Ancient Conspiracy.
He does, however, have some (possibly laser guided) amnesia. It's possible that recovery of those memories would return him to a cackling evil mad scientist of epic proportions.
Very, very morally ambiguous indeed. It seems he used to be highly arrogant and not always that concerned about ethics or possible consequences, and that he did do terrible things (including complex drug tests on children). However, it also turns out that most of those terrible things were done with good intentions and that he now feels extremely guilty and tries to atone.
Power Rangers RPM's Dr. K, who was raised by Alphabet Soup operatives for weapons research and development. Although she's technically one of the "good guys," in a textbook case of Nice Job Breaking It, Hero, one weapon she created in particular—the Venjix computer virus—becomes the season's Big Bad after she uploaded the virus to blind Alphabet Soup's security servers in a failed attempt to escape her imprisonment. She spends her life afterwards trying to make up for her mistakes.
Choujuu Sentai Liveman had five villains who qualified as this, with the Big Bad being named Great Professor Bias and his human students named Dr. Kemp, Dr. Mazenda, Dr. Obular, and Dr. Ashura. Also, while it isn't in their names, the aliens Guildos and Butchy probably count, as well. While Bias proves to be irredeemable, Kemp goes insane, and Guildos just dies too early, all of them make Heel Face Turns at some point.
If you're a doctor in a Kamen Rider series, you're probably not a nice guy.
Doctor Shinigami/Ikadevil was one of the main generals of the original Kamen Rider series.
Kamen Rider Double has Dr. Isaka/Weather Dopant, who actually modified Gaia Memories to kill their users so he could take them and incorporate them and their powers into himself later on, and Dr. Prospect/Eyes Dopant, who performed horrifying experiments on children to turn them into psychics, planned to kill the failed subjects by electrocution, and planted eyes on them to watch them and kill them if they strayed out of the village. Prospect was responsible for the Despair Event Horizon of Katsumi Daido, the antagonist of the first W movie "A-to-Z: Gaia Memories of Fate".
The titular Doctor of the Sid & Marty Krofft series Dr. Shrinker. His theme song even states that he's a madman with an evil mind.
It's been noted on The Big Bang Theory that Doctor Sheldon Cooper is "one lab accident away from becoming a super villain" (which makes the page quote deliciously ironic). Leonard's mother, Dr. Beverly Hofstadter, can give you the closest thing to Mind Rape a sitcom grounded in something resembling reality can offer via her questionable usage of her psychiatrist skills. Dr. Amy Farrah Fowler, while usually seeming to be less likely to snap than her boyfriend and Distaff Counterpart Sheldon, has offered to have her lab monkeys kill someone more than once. Dr. Bernadette Rostenkowski-Wolowitz's work for a lab private pharmaceutical company supposedly curing diseases is also implied to be morally ambiguous-which is scary because she's always smiling
Bernadette: Oh, I take pacts very seriously. One time at my lab, a petri dish of genetically modified super-virus went missing. That day we made a pinky swear never to admit we crossed Ebola with the common cold.
Howard: Why the hell would you cross Ebola with the common cold?
Bernadette: We never did. (beat) That would be a terrible, terrible thing.
In Helix, this is Implied of all the research scientists who work at the Arctic Biosystems base. All of them hold the title "Doctor," and come there to take advantage of the opportunity to perform research unencumbered by regulatory agencies. Lead researcher Dr. Hiroshi Hatake openly admits that he encourages his people to "push the envelope."
Sir Wilfred P. Hufflebaggins III from Tom Smith's filk album "The Last Hero On Earth" - Very Evil. And don't forget, he's SUBTLE! That's why you've never heard of him.
They Might Be Giants: Doctor Worm: He's not a real doctor, but he is a real worm, he is an actual worm.
Doctor Steel: No one's sure what he's a doctor of, exactly (he's said he's a Doctor of "Reality Engineering"); but he's bent on taking over the world using an army of robotic toys and brainwashed "toy soldiers" so that he can make the world a better place (for him).
Disc jockey Dr Demento plays some.. interesting.. songs on his show.
"They're coming to take me away, uh-huh. They're coming to take me away, ho ho, heehee, haha, to the funny farm, where life is beautiful all the time and I'll be happy to see those nice young men in their clean white coats and they're COMING TO TAKE ME AWAY HAHAAAAAAAAAAAAAAaaaaaaa..."
Doctor X from Queensr˙che's concept album Operation: Mindcrime has one.
He didn't come up with the name himself. He was a champion high school wrestler in Oklahoma during the 1970s, but broke his nose once during a match, and came back wearing a hockey mask the next night, with a local sportswriter calling him "Dr. Death."
TNA: Dr. Stevie. Evil psychiatrist, has a habit of brainwashing his patients to become his submissive lackeys. Also probably not a real doctor, since his ECW and WWE past is mentioned.
Kaiju Big Battel: Dr. Cube. Evil, trying to take over the world with an army of genetically-modified Kaiju.
Formerly known in Memphis as Downtown Bruno, Bruno Lauer arrived in WWE in 1991 as Dr. Harvey Wippleman.
Best known as Eugene in WWE, Nick Dinsmore has competed for TNA's India promotion Ring Ka King as Dr. Nicholas Dinsmore.
Adventures in Odyssey had the evil Dr. Regis Blackgaard. Not sure what he's a doctor of. When his "good" identical twin brother Edwin came to town he introduces himself as "Mister"; Lucy, mistaking him for Regis, asked if he had to give the title back because he was evil.
In Round the Horne, a recurring villain was Doctor Chu-En Ginsberg, M. A. (failed).
The rather ironically-named Dietrich "Medic" Luzweit in Dino Attack RPG would certainly qualify, being an unstable doctor who nearly lost his medical license after somehow removing a patient's skeleton. The only thing that kept him in action was the fact that a mutant dinosaur apocalypse had just started and there was a desperate need for people with medical training. Averted by just about every othermedic in the RPG, though.
From Warhammer Fantasy the Skaven scientists mostly make hideous mutants and terrifying war machines.
Fabius Bile, a geneticist who's reduced planets to shambling mutants and created a race of murderous superbeings. In battle he shoots people with syringes that can make them explode. He's also thousands of years old, preserved by Black Magic pumped into his veins, and doesn't worship any of the Chaos Gods despite extensive dealings with them, which may actually be scarier than any of his other accomplishments.
The Dark Eldar Haemonculi, from whom Bile actually learned his skills. They're functionally immortal Mad Scientists that specialise in all kinds of body modifications, from replacing their own blood with acid to turning people into horrible biomechanical abominations. In battle they wield all sorts of freaky weapons, from guns that fire their own acid blood at enemies to syringe-gauntlets that cause the victim to grow out of their skin and caskets filled with invisible fiends that strip the flesh from their victim's bones.
Ork Mad Doks/Pain Boyz are no more evil, and quite a bit more eccentric than other Orks. Probably Chaotic Neutral if pressed.
The Savage Worlds plot point campaign Necessary Evil features Dr. Destruction as the leader of Omega, and includes lesser villains like Dr. Devolution. The entry for the last one lampshades the fact that so many supervillains had doctorates.
Champions has the master villain Doctor Destroyer, who actually does have multiple earned doctorates (under his real name). Any adventure he's involved in is likely to end up with dead superheroes.
Evil. He sells his soul to the Devil, for Knowledge and Power and Helen of Troy. Very Mad Scientist because Knowledge is one of his goals.
Or, ambiguous: in some versions, he has his 7 years of Glory, and goes to Hell, ha ha ha, serves him right for being Evil. In some versions, Faust is presented as a sympathetic Character who wants to be redeemed: when he fails, it is tragic Grand Opera, when he succeeds, it is happy ending Light Opera. Goethe has him as Distracted Neutral if not Chaotic Neutral more than anything else. He sells his soul for knowledge, and most opera versions of Goethe end right after Mephistopheles has done his job by pushing Faust firmly over the Moral Event Horizon. At the end of the second half, after much weirdness, Faust a Heel-Face Turn because he looks around and then gives himself a What the Hell, Hero? speech.
Doctor Miracle from act III of The Tales Of Hoffman. His plot is to get the sick Antonia to sing herself to death. It takes place in Ancient Greece, so it would've been when the Hippocratic Oath was fairly new.
Advertisements for the Doctor Dreadful line of toys feature a goofy Mad Scientist named, well, Doctor Dreadful. The line includes the "Doctor Dreadful MD" toys, where the character claims the "MD" stands for "Monster Doctor". (And in one commercial, he produces a sheepskin to prove he is, indeed, a licensed Monster Doctor.)
Deus Ex: Dr Jaime Reyes. Good guy. Dr. Megan Reed. The jury is still out, but evidence heavily suggests she's very amoral.
Resident Evil: Dr. William Birkin and Dr. Alexia Ashford: The former being a megalomaniacal scientist who starts getting crazy about his research, which causes people to turn into zombies, and eventually causes the outbreak. This makes it okay to shoot him. The latter is another scientist who is also crazy about her designed virus, but also wants to rule the Earth. This also makes it okay to shoot her.
Psychonauts: Dr. Loboto, who harvests the brains of young psychic children and attempts to put them in psychic-powered tanks. His PhD is in dentistry, however, which makes one wonder why Coach Oleander has him working with brains.
Half-Life 2: Dr. Breen, if not evil, then still the willing head of a puppet government.
Sonic the Hedgehog has Doctor Ivo "Eggman" Robotnik: Evil. Nobody has any idea what Ivo's doctorate is in. Probably engineering, if the robots he designs are any indication.
Mega Man: Dr. Albert W. Wily: Evil, but his creation Zero wound up fighting for the side of good.
The classic series likes to play with this. Dr. Wily plays it straight, Dr. Cossack subverts it because he was blackmailed into it by Dr. Wily kidnapping his daughter, and Dr. Light not only outright inverts it, but he serves as Dr. Wily's good counterpart.
Mega Man Zero: Dr. Weil: Waaaay more evil than Wily could ever hope to be. Definitely among the most evil on this list.
Cave Story: Dr. Fuyuhiko Date: As evil as they come. Master of the Player Punch. Actually is a medical doctor.
Dr. Baldhead, from Guilty Gear: Evil, murderous, insane; a medical doctor as well. It's implied that he does a Heel-Face Turn later in the series, but when he does, he changes his name to Faust, dropping the Doctor from his name. However, as he still practices medicine, other characters call him "Dr. Faust".
From the Spiritual SuccessorBlazBlue; Dr. Litchi Faye-Ling: Good, compassionate, medical doctor, but corrupted with the Boundary, and currently amongst the antagonistic NOL, with Hazama around and her morality is in danger whether it will plummet hard to complete evil thanks to Hazama's influence, or she will retain it and consider it a Dirty Business to save the one she loved and herself.
Also from Blazblue, Relius Clover. Relius.Freaking.Clover. While never expliciltly stated to have a doctorate, he is a master of science and alchemy, creating clones and Magitek weaponry. He's also a complete sociopath willing to torture people in an almost rape-like way, kill his own wife and daugther to turn their corpses into living weapons, and work with Hazama to try and destroy all reality just to see what happens next. Though strangely, he has no 'Doctor' title, but another.
In a subversion, Mad Scientist and Big Bad Caulder/Stolos from Advance Wars: Days Of Ruin was revealed to have been a doctor, but he doesn't use the prefix — he was kicked out of the medical academy for ethical violations. He's just THAT evil.
In addition to being a hilariously over the top Spy Fiction game, Metal Gear Solid deals a lot with questions of ethics in extreme situations. As a results, the series has lots of scientists with highly morally ambigous pasts and presents.
The prime example in the series and for the trope in general would be Dr. Naomi Hunter. She is introduced as the medical advisor for the opperation on Shadow Moses, but is actually an agent planted by Ocelot. She murdered people, send people who trusted her into ambushe, and handed vital technology over to the enemy. Then she repents and helps snake, disappears from prison, joins Ocelot again and develops weapons for him, and then has the guts to ask Snake to rescue her. Then she becomes Otacons girlfriend and betrays him and Snake by stealing important data for Ocelot, again! She then switches sides again to help Snake a last time and commits suicide. And all the time she seems to be genuinly sorry for what she did, but would do the same things again without hesitation. And she never really explains what she is trying to achive.
Para-Medic starts as a genuinely nice young physician, but somehow got forced to sign up with the team in MGS3 after the events of the Virtuous Mission, or would have had her license revoked (although she hints that she intended to do the mission anyways). MGS4 later reveals that she was Dr. Clark, who created the clones of Big Boss and made Grey Fox into the Cyborg Ninja against his will. She got killed by Gray Fox as payback for what she did to him, and partially after EVA/Big Mama told him that she was one of Zero's Patriots and told him to kill her.
Also Otacon is in fact Dr. Hal Emmerich. While a good guy, he was too naive to realize he was building a superweapon, and after going underground with Snake, he frequently broke into high security military computer networks to steal intel and blueprints for Snakes gadgets. Even before meeting Snake, he has done a few instances of hacking into high security networks: One instance was when he hacked the FBI's central database while he was within the Engineering Research Facility branch of the FBI, which got him fired.
Dr. Emmerich, Hal's father, was similar. Although a good guy, he did work with nuclear weapons and was involved in a project to create a perfect deterrent. Although he was initially willing to work on the project, it was only because he legitimately believed Coldman when he said that it wouldn't be used even once. Unfortunately, Coldman proved his lying/insane nature when he intended to launch a live nuke to test its retaliation abilities.
Strangelove worked with AI development, and also did torture to Snake, although it is implied that she personally felt disgusted at herself for having to resort to torture. In addition, she intended to create the Mammal Pod so she could revive The Boss, find out what really happened in Operation Snake Eater, and clear her name. Her working to develop the Peace Walker weapon was moreorless a necessary evil she had to put up with in order to do it.
"Doktor" from Metal Gear Rising: Revengeance also displays a rather distressing lack of both regular ethics and medical ethics considering he's supposed to be one of the good guys.
The Medic of Team Fortress 2: Likely a confirmed doctorate, given that most of his team-mates refer to him as "Doctor", "Doc", "Herr Doktor" and the like. Fully aware that healing his team (actually a side-effect of his Medigun) means that they are that much more efficient at killing the other team. By the way, his bio states he never took the Hippocratic oath. And TF Industries still hired him.
The Engineer's backstory says he has 11 Ph.D.s, and he seems to be a much more stable guy, although that's not saying much considering that the flavor text for The Gunslinger is that he chopped his own hand off and replaced it with a robot replacement For Science!.
Doctor Killjoy from The Suffering, a 1900s level doctor who kills most of his patients in attempts to cure their mental problems. Like Josef Mengele, but British, and he can come back from the dead. EVIL! Still, he apparently has a genuine desire to help Torque with his problems even through extreme means.
Though never called a doctor outright, you'd have to have a couple doctorates in badass to engineer MULTIPLE plagues which nicely complement each other, as Hakke Dal from Maken X (Maken Shao on Playstation) so capably demonstrated. Also he shows he has no moral compunction against killing his own daughter should you brainjack her to use against him. The reason she was trapped in a psych ward in the first place was because he tested the one of the first prototypes of the Uvad virus on her. He'd likely be BF Fs with Killjoy above in his college days and may have even roomed with him. Also, he's an oddly black man in a game world full of greys. (Though all Hakkes intend to kill a lot of people to forwards their utopia, Dal seems to be the only one enjoying his work. Margaret is just Ax-Crazy and hopped up on designer drugs like Eugenics and Relativism. Big Bad Geist is actually one of the sanest members of the group, as both he and right-hand Yusef can be diplomatically reasoned within a couple endings, provided you made the appropriate storyline choices.)
Surprisingly, even World of Warcraft has a few of those. Most of them are undead. However, the two who really stand out (both of them evil) are not. Scholomance boss, human, utterly insane, Doctor Theoden Krastinov (doesn't help that his title is "The Butcher"). More badass, gnome Dr. Weavil, obviously a blatant parody of Dr. Evil. He even has a minion called Number Two. No Mini-Me unfortunately...
Doctor Thrax from Command & Conquer: Generals is quite evil, or at best a religious extremist a laOsama bin Laden. He wants you to tell stories of your defeat to your three eyed grandchildren. He also wonders if he shouldn't have gotten his degree from a mail-order college. He specializes in bioweapons.
Tekken: Dr. Boskonovitch: Mad Scientist, generally shown somewhat on the side of good (ally of good-guy Yoshimitsu, for one).
Dr Abel: Evil. What kind of monster tries to blow up an innocent 400lb cybernetic killing machine with no voice? (I'm serious... it's complicated. A.I. Is a Crapshoot, folks.)
Borderlands: Dr. Zed: The last person you want near you with anything sharp, but one of the very few people that you can rely on in the Death World that is Pandora. May or may not have somehow been responsible for a Zombie Apocalypse.
Possibly a subversion, given that Zed doesn't actually have a medical degree and references this frequently (who needs one when you've got style?). In the sequel, he has a rival in Doc Mercy, who, to Zed's frustration, does have a degree, but is also a bandit and far more concerned with making wounds than treating them.
Dr. R. Muckly, who you have to rescue from the Vietcongs in NAM-1975. It turns out, in a rather screwy manner, that he is a Mad Scientist who wants to use a Kill Sat to take over the world, and so you have to fight him as the game's final boss.
Mass Effect: Dr. Mordin Solus. Before you actually meet him, all you have is a name and the space station he can be found. As you investigate, everyone tells you that he's crazy and that they don't expect you to survive the encounter, the tales getting more horrid every time.
"He's not just a doctor. Doctors don't execute people and display their bodies as a warning."
When you meet him, he turns out to actually be quite crazy, but seems to be fully aware of what's going on around him and a genuinely nice person. He also seems to be a former member of the salarian Special Tasks Group and has tech powers to burn people alive.
And he is also revealed to be one of the leading scientists who spent some time re-engineering the genophage, an incurable genetic disease that causes massive rates of miscarriages in pregnant krogan to keep the numbers of the species low. He's aware that the bioweapon was ethically reprehensible, but does not regret his actions. He mentions that he started the clinic in Omega specifically so that he could do something less morally ambiguous in his twilight years.
Also, Dr. Saleon. Need spare organs? Grow them in the natural environment of a subject's body!
Dr. Hojo from Final Fantasy VII. Quite. Crazy. It's hard to find anything he did that is not For Science!. Arguably responsible for every single calamity that happens in FFVII universe.
Except Jenova. She fell before he was born. However, he did contribute greatly to making Jenova problem far worse (can you say Sephiroth)?
BioShock: Dr. Suchong: Absolutely mercenary at nature and willing to commit scientific atrocities as long as he's paid well in the end.
Dr. Tenenbaum: Created the Little Sisters and initially ambivalent since it's all For Science!. Eventually develops a maternal instinct and becomes The Atoner.
Dr. Lamb: Enemy of Free Will and devoted to the destruction of individuality.
Dr. Steinman: Lethally experimenting on people in order to satisfy his twisted perception of beauty. Evil and completely out of his mind.
Zahra from Suikoden Tierkreis, who is always a little too excited to dissect examine every non-human specimens in your base.
Dr. Keith Fetus from Meat Boy series who is on evil side. In Meat Boy universe, you don't even have to be born to get a university degree.
Dr. Balfour and Dr. Neis from Tales of the Abyss, who between them created fomicry in the form we currently know it. They split sides into good and evil when Balfour who had since been adopted by the Curtiss military family and taken their surname gave up his research and declared a ban on fomicry, but Neis refused to do the same and joined the God-Generals so that he'd have the resources to continue.
League of Legends has Dr. Mundo, The madman of Zaun. As stated in his bio: In his eyes, you are already dead.
Fallout 3: In a game filled with sociopaths, Dr. Stanislaus Braun does his best to stand out: As controller and inhabitant of the Vault-112 virtual reality simulations, he has been continually torturing, killing and reviving the other inhabitants of the simulation for 200 years, just to amuse himself. The only reason he enjoys this is because they're real people, not just computer programs; if you Mercy Kill everyone else there so they can't be revived, he'll act like a spoiled 10-year-old and get upset that you took away his toys. The fact that you've doomed him to being stuck alone in the simulation forever doesn't really register. When you get trapped in Vault 112, he offers to let you leave.... but only if you murder everyone else in the vault for his amusement.
Ansem Retort's Dr. Zexion Doreone: A complete and utter Jerk Ass who once implanted an Oreo in one of his patients for no apparent reason; the Oreo fused with his DNA somehow, so the patient became half-man, half-cookie. He also planted a firecracker in Riku's liver, fashioned a new heart for Riku out of bendy-straws and a Hot Pocket, and replaced another guy's lung with a monkey's ass. Then there's the fact that during his time as Governor, he's been implicated in 5 sex scandals and 3 murder scandals. The only other person on the cast who likes him is Axel, who happens to be a sociopathic serial killer. Everyone else puts up with him only cause he's part of the cast.
Doctor Narbon of Narbonic: Helen is Evil with a capital E. A rare female example; most supervillainous doctors seem to be men. Her clone "Beta" is cute-evil - aspires to evilness and has the reputation and imagery down, but never got around to actually pulling anything off.
Dr Edward Upton from Misfile, the protagonist’s father. He's a gynecologist who tends to creep out Ash's friends by remembering the details of their... ahem....girl parts.
Hanna Is Not a Boy's Name: Doc Worth hasn't even actually got a doctorate; he dropped out of medical school. He doesn't let that stop him practicing medicine, and he's also terribly shady just generally. Hanna even implies that he developed a crush on Conrad because Conrad beat him up. And then there's Hanna's freaking torso, and the "classified" procedure Worth decides Hanna needs after being attacked by a ghost. It seems to be working out all right for Hanna, so, cool, but, also, WTFFF.
Vigil: Myriam seems to be a fairly benign version. She doesn't actually have a degree, due to being kicked out of medical school for failing the psychological test. And she's learned most of what she knows by robbing graves.
In Cuanta Vida, the Blue Doctor is insane and many of his teammates don't want to get treatment from him or people will fetch his patients after the procedure to keep the doctor from performing "extra tests". He kills Liam and tries to kill Jeremy for being crippled and, in his opinion, useless. If he kills them, they would have been replaced.
The facility in which the entire story of Ruby Quest takes place in, known as The Metal Glen, was—in a nutshell—built out of an odd, isolated, geological-formation from out in the middle of a secluded loch for the specific purpose of doctors and medical researchers practicing/ testing treatmentsnote (treatments that would likely be deemed as "unconventional" by most) without the need of the proper permits, license, or the possibility of criminal prosecution.
lonelygirl15: Dr. Calvin Hart: Debatably good, but fairly creepy.
At least until Penny dies, at which point he starts playing this trope dead straight.
Actually, this trope is deconstructed: He only becomes evil because Captain Hammer thinks all smart and nerdy guys are evil, and thusly treated him as a villain even when he was not yet one, so he became a villain because he was seen as a one anyway. And he is still better than Captain Hammer
Dr. Insano of The Spoony Experiment, nemesis of Linkara and alter ego of Spoony. His running mate is Fu Manchu.
And he wants to take the world (of course!)... WITH SCIENCE!!!!
Dr. Insano's brother, Dr. Linksano of Atop the Fourth Wall, has now been created due to a crossing of parallel dimensions brought on by Dr. Insano during the Spoony-Linkara review of Warrior #1. The sequel to said review introduces the Insano equivalents of several That Guy with the Glasses regulars, including The Nostalgia Critic, Film Brain, and...Beary (who uses a mind-controlled Benzaie to get around).
Dr. Tran. Not only is he a REAL DOCTOR (from AMERICA), he's a dashing secret agent with a PhD in KICKING YOUR ASS!
In the Global Guardians PBEM Universe, no one is really sure what specific areas Doctor Heinrich Frankenstein, Doctor Phillipe Moreau, Doctor Blight, Doctor Sinister, Doctor Emilio Astonishing, Doctor XX, Doctor Devastation, Professor Sunday, Professor Septimus, Professor Penelope Periwinkle, and Doctor Gavin von Leggend (all villainous Mad Scientists) hold their degrees in.
SCP Foundation: SCP-231 is a woman who can only be attended by medical personnel who haven't taken the Hippocratic Oath. Why? Because she has to be permanently strapped to a hospital bed, and once daily she has to be subjected to a medical procedure so horrific that most of the details can't be disclosed or else she gives birth to...something which could cause untold death and destruction.
Dr. Wondertainment, a person or organization dedicated to creating ridiculously dangerous toys and distributing them among children. Apparently more oblivious than evil.
Chromedome: Bah! More varm fuzzy nice-nice! Vot good is science if no one gets hurt?! You should all be ashamed of yourselves!!! Vat vith your vorld peace und your moccasin valking und your potpourri! You are not mad scientists; you are a bunch of hippies!!!
Doctor Venture: Kinda Good. He isn't plotting world domination or looking for dogs to kick, but he is a bitter grouch at the center of a Sadist Show. And he did once build a wish-fulfillment machine that was powered by the heart of an orphan. ...and then there was the bit with reanimating the corpses of his enemies (and implied killing of the cloned bodies of his children) and selling them to the army. He isn't actually a doctor.
Dr. Byron Orpheus: Good, but obnoxious and overbearing, and not above mind-wiping his own daughter repeatedly so she'll forget that her closet is the doorway to the underworld. He has a degree in Women's Studies, but accredits his Doctorate to a higher power.
The Phantom Limb was a professor before his lab-accident-powered Face-Heel Turn, and likely had a doctorate.
Dr. Mrs. The Monarch: Not only evil, but better at it than the Monarch himself.
It is later revealed her Doctorate is Honorary from donating money to a Evil College.
Doofenshmirtz: *shows diploma* They don't give these out to just anyone, you know.
Vanessa *reveals price tag* Anyone with fifteen bucks, they do.
Doofenshmirtz: That's enough looking!
Dr. Nick Riviera, aka "Dr. Nick" on The Simpsons. Not truly evil, but clearly missing a few marbles, something his patients often suffer as a result of. He actually went to medical school (proven by a flashback) but it isn't known if he actually graduated, and while he practices medicine, he uses controversial and often illegal methods. To give some examples, in one episode a hospital review board brings up the accusations against him which include performing surgery with a knife and fork from a seafood restaurant and misuse of cadavers (he had put them in his car in order to use the carpool lane and get to work quicker). In another episode, he is asked to talk to the coroner, and he says, "Ugh, the coroner. I'm so sick of that guy!" suggesting his patients get sent there rather often. (Ironically, this is the episode where Nick does Homer's double bypass surgery, and Nick actually does it right, but Lisa helps him a little.)
Dr. Julius Hibbert, post-Flanderization, can also qualify as being weaselly, up to the point where you may argue he's sort of evil. Originally, Hibbert was one of the few competent people in Springfield and often played the role of Only Sane Man, but Hibbert eventually became a doctor who seems to spend more time finding ways to have his patients sign away their right to sue before the inevitable malpractice issue than actually being a quality doctor. And he also profitted heavily when all companies in Springfield eliminated their health care programs, forcing people to pay at a premium.
South Park: Professor Chaos: Evil, but harmless. Not actually a professor, but rather Butters wearing tinfoil.
Futurama: Professor Hubert Farnsworth: Senile to the point of insanity, but mostly harmless. Has a penchant for creating doomsday devices, only keeps Amy around because she's his blood type, tries to harvest Leela's organs, is implied to be a cannibal, implanted Hitler's brain in the body of a shark, killed people for their stem cells, has been frequently cited for public nudity, and frequently, knowingly sends his crew on life-threatening adventures without warning, to the point of hiring replacements even before their demises are confirmed. In his youth, he created the modern robot, an ecological disaster. Opposed the legalization of Robosexual marriages, but eventually changed his mind.
YouTube Poop: Doctor Rabbit: Evil as sin. Also, he is an actual doctor. Well, a dentist, but still...
Herr Doktor from ReBoot. Obediently Evil. Whenever Megabyte needs to have something nasty done to a prisoner, this is the binome for the job.
Adventures of the Galaxy Rangers: Dr. Owen Negata of BETA. Casually talking about using a teenaged boy as a control for a genetic experiment will land you here. Funny thing, he's considered one of the good guys. GR could be a real World Half Empty.
Clearly referenced in the Arthur episode "Elwood City Turns 100!" When the class is being handed their roles in the town's centennial play, Buster misreads "Director" as "Dr. Ector" and immediately assumes he's the villain. And has a claw. When Buster later makes a surprise appearance on stage as an alien named Dr. Ector, he's not villainous, just oddly obsessed with dental hygiene. It Makes Sense in Context.
Parodied in the "Dark Bunny" tv show. His arch-enemy is the "Doctapus," an octopus who apparently went to college and earned a doctorate.
Not to be outdone, the Transformers Generation 1 cartoon 3-parter "The Ultimate Doom" had Doctor Arkeville, the self-proclaimed evil genius who assisted the Decepticons in developing a microchip that could control human minds.
Speaking of Transformers, Rescue Bots features the amoral, scheming, self-aggrandizing Doctor Thaddeus Morocco, voiced by Tim Curry.