Both Masego and Wekesa from A Practical Guide To Evil. Not surprising given that they are both Villains with Names strongly associated with magic, in a world where magic is commonly used in place of technology even for things like grenades. Both have stated outright that they are more interested in tearing apart Creation to figure out how it works than in gaining temporal power.
The Radix: Edgar Wurm, a cryptoanalysist who managed to decode the Voynich manuscript, but in the process got mad and obsessed with the Radix.
In Terry Pratchett's Discworld books, the Alchemists' Guild are also Magitek mad scientists. Inverted with the character of Jeremy Clockson, who has the detachment from reality and dangerous obsession of the typical Mad Scientist because (most of the time, and in a very specialised way) he's saner than normal people.
The Igors of the Discworld series. Though typically the assistants of a Mad Scientist, they're known to conduct their own experiments, such as growing noses with feet, and their own special version of "self improvement". Though to be fair, the Igors in general are remarkably Genre Savvy — they know their place in the chain, and how to react when that chain is shaken. In fact, the clan foists off the most "modern" variant of their clan upon the Night Watch in an attempt to cease the corruption: that is to say, Mr. "Noses with Feet". Similarly, in Carpe Jugulum, an Igor working for vampires revolts at their innovations and revives the old master — not so much reviving the Good Old Ways as the Moderately Less Odious Old Ways.
Bergholt Stuttley "Bloody Stupid" Johnson may qualify, aside from his architectural and landscaping mishaps he made a mail-sorter with a wheel that has pi as exactly 3, it started churning out mail from the future and alternate universes until the post master smashed it.
Leonard of Quirm, an exceedingly gentle, patient genius, isn't so much mad as unable to foresee the consequences of his inventions.
While the Mad Scientist might seem quintessentially modern, he's probably Older Than Steam. The inspiration for both Mary Shelley's novel Frankenstein and the adaptations which distorted Frankenstein into a Mad Scientist came from a much older literary and popular tradition about Mad Alchemists, and their blasphemous, yet entertaining, obsessions with the creation of homunculi and the secrets of eternal life. The most well-known remnant of the old "Mad Alchemist" trope today is the Faust myth, and its literary adaptations in Marlowe's Doctor Faustus and Goethe's Faust.
An interesting fact is that the 1910 silent film Frankenstein features a scene of monster's creation that is highly relevant to an alchemical procedure of palingenesis (re-formation of a once-living organism from its ashes or from its severed parts by heating). No other film adaptation involves this trace.
Victor Frankenstein, as originally conceived in Mary Shelley's novel, was not quite a Mad Scientist. Although he sees himself as a descendant of Mad Alchemists, Shelley makes his character more rounded and his mental instability more subtly portrayed. However, within decades wildly popular nineteenth-century melodrama theatre adaptations recast him as a cackling Mad Alchemist.
While he's not a Mad Scientist throughout the novel, he certainly is one when he's actually working on bringing his creature to life:
My cheek had grown pale with study, and my person had become emaciated with confinement. Sometimes, on the very brink of certainty, I failed; yet still I clung to the hope which the next day or the next hour might realize. One secret which I alone possessed was the hope to which I had dedicated myself; and the moon gazed on my midnight labors, while, with unrelaxed and breathless eagerness, I pursued nature to her hiding-places. Who shall conceive the horrors of my secret toil as I sabbled among the unhallowed damps of the grave or tortured the living animal to animate the lifeless clay? My limbs now tremble, and my eyes swim with the remembrance; but then a resistless, and almost frantic impulse, urged me forward; I seemed to have lost all soul or sensation but for this one pursuit. It was indeed but a passing trance, that only made me feel with renewed acuteness so soon as, the unnatural stimulus ceasing to operate, I had returned to my old habits. I collected bones from charnel-houses and disturbed, with profane fingers, the tremendous secrets of the human frame. In a solitary chamber, or rather cell, at the top of the house, and separated from all the other apartments by a gallery and staircase, I kept my workshop of filthy creation: my eyeballs were starting from their sockets in attending to the details of my employment. The dissecting room and the slaughter-house furnished many of my materials; and often did my human nature turn with loathing from my occupation, whilst, still urged on by an eagerness which perpetually increased, I brought my work near to a conclusion.
Professor Butler in Feliks, Net & Nika. He's biology teacher, but... unusual one. For one, he keeps herd of small tarantulas and python named Tape (because he was so thin when he was little. Now they should change his name to Hawser). Next, he's conducting his own freaky breeding and genetic experiments on plant. Among nice things like beautiful flowers that can grow only in human hair, there are plants that seem to be sentient and one giant sundew that is definitely sentient and wish to befriend humans. Actually his creations are rather benevolent... but try to believe it when man-sized plant with More Teeth than the Osmond Family is smiling at you.
The King of the Mountain in Enid Blyton's The Mountain of Adventure.
The stories From Beyond, like At the Mountains of Madness, The Dreams in the Witch House and The Shadow Out of Time. While all of the above feature scientists, only the one in From Beyond is a genuine Mad Scientist. Though some of the others Go Mad from the Revelation, they never adapt Mad Scientist mannerisms, instead getting more realistic nervous breakdowns.
Herbert West, mentioned above in the Film of the Book (albeit updated to later in the 20th Century.)
Arthur Machen's The Inmost Light written in 1894 contains a rather horrific version of this trope.
There's one in The Great God Pan. While the novel seems desperate to make him slightly sympathetic, at least to a modern reader he comes off as a monster. Yeah, practice some experimental brain surgery with a teenaged girl completely infatuated with you, and clearly incapable of truly informed consent. What could go wrong?
The villain of Hilari Bell's The Last Knight is a rare example of a mad scientist in a fantasy setting, performing dubiously ethical experiments in order to give magical powers to humans (as, in the story's universe, only plants and animals have magic).
The Star Wars Expanded Universe introduce Qwi Xux, an incredibly brilliant scientist who designed the laser for the Death Star, the World Destroyers, the Sun Crusher and a number of other dangerous creations. Unlike many others in this trope her extremely guarded upbringing (she was raised by Imperials in an oppressive cram school where the price for failure was your hometown being obliterated) has caused her to develop a very naive and innocent view of her creations, having been led to believe they were intended for industrial applications (the Death Star would blow up a massive asteroid which the World Destroyers would then be able to harvest for materials, etc.).
Subverted to some extent in the George R.R. Martin-edited Wild Cards books. There are Mad Scientists a plenty, on both hero and villain sides. Or at least folks who have been infected with the wild card virus who are now determined to build androids, giant mecha suits and all manner of mad-sciencey devices. The kicker is that the inventions they create really are just piles of unworkable junk, and the particular power they have developed is the ability to make their crazy inventions work. Any attempt to analyze and reproduce the devices prove to be fruitless and show that there is no way they should function in the first place.
Professor Drummond from the Nick Carter short story "Nick Carter and the Professor" from 1902. This story appeared in the reprint anthology Nick Carter, Detective published in 1963 by the MacMillan Company, with an introduction by Robert Clurman. Drummond worked out of Malden, MA and had his underlings steal a body from Mount Auburn in Cambridge. Carter also faced Dr. Jack Quartz.
In A Fighting Man of Mars, Phor Tak. Originally sane while making his inventions, but losing it after being maltreated and exiled by his jeddak. At first it appears to be Revenge, but in the end, he reveals he wants to Take Over the World.
Garfield Reeves-Stevens' novel Dark Matter features a mad scientist cum serial murderer who actually manages to endow himself with metahuman powers similar to Captain Atom, Doctor Solar, Firestorm, and Doctor Manhattan (in imitation of the latter, he even visits Mars).
Remo Williams has encountered mad scientists, for example Dr. Judith White, who mutated herself into tiger/homo sapien hybrid.
In the Soviet science-fiction story Amphibian Man, the title character's adoptive father, Dr. Salvator gives him shark gills, extensive knowledge about Oceanology and other sciences... and none whatsoever about such pesky details like days of week. Salvator also gives a rather passionate speech toward the end of the book critizising Science Is Bad.
Saruman in The Lord of the Rings can also be viewed as this character type, what with his obsession with industry at the expense of the natural world. He is also something of a would-be Emperor Scientist; he would have become one had his whole Take Over the World plan gotten off the ground.
The Corsay Books have a wide variety, from Frankenstein-style reanimationists, to those dabbling in Alien Geometries, to specialists in disciplines that seem closer to magic. They are the main antagonists of the work, but generally portrayed as misguided and dangerous rather than evil.
And he had to hide his genius or use it to play tricks with, when, with an ordinary face, he would have been one of the most distinguished of mankind!
The main character of The Chronicles of Professor Jack Baling is one of these. He doesn't start off as one, but by the end of the first episode, he resides firmly in this territory. There seem to be some other characters who are also Mad Scientists, but we haven't seen them in any great detail yet.
From The Dresden Files: Storm Front, the main antagonist has a whole factory producing a magically-laced drug. It's catalyzed by a ritual, fueled by sex.
Dr. Sacreya of Sacreya's Legacy is certainly mad, creating a zombie virus and all, but his intentions are good.
The Rings of Saturn has an old, very much insane scientist, living in the abandoned part of a space pirate base (without their knowledge) who is obsessed with researching other dimensions (and doesn't hesitate to send his lab assistant, or random strangers into them. Without giving them a way back.)
Ex-maester Qyburn of A Song of Ice and Fire is definitely this. He lost both his chain and the title of "Maester" when the Citadel found out about his anatomical experimention on still-living people. After that, he found employment with the BloodyMummers — and fitted himself right in. When he got the chance, he switched gears and leapt at the opportunity to work for the Lannisters either as a still-very-excellent surgeon or a Torture Technician — whichever. And, from the chapters in King's Landing, we get a good idea what his earlier experiments involved and were geared towards... Let's just say that his creation of a Frankenstein-like, zombie-like creature mostly made up of Gregor Clegane is just the very tip of the nightmare-inducing, death-defying, beyond-the-bounds-of-medicine iceberg. *shudders*
The aeshes of A.L. Phillips's The Quest of the Unaligned have this reputation, and in fact in magickless Tonzimmiel, "aesh" means "certified engineer." Word Of God reveals that their secondary power is Haesh's Trace, a burst of insight that grants them true understanding of something they've been considering. An example of this is seen in Laeshana's sudden insight into the nature of magic while she is finishing her studies at the College of Magic.
The Solarian roboticist Jothan Leebig in Isaac Asimov's The Naked Sun. He's revealed to have been working on bypassing the First Law of robotics which prevents robots from harming humans by exploiting a flaw in the wording of the law. Leebig uses this to successfully plan and execute the murder of his colleague Rikaine Delmarre, who strongly disagreed with his vision, and attempt to poison both the newly assigned Solarian police investigator and Elijah Baley - the Earth detective. When he's forced into confessing, he also admits to have been planning on developing and building new war spaceships using this same exploitation of the positron brain in order to turn them into very dangerous and effective weapons.
Willy Wonka may be a cheery candymaker, but his amazing sweets and otherwise largely stem from mad science (his favorite room in the enormous factory is The Inventing Room where he works on new creations). Over the course of the original novel and its sequel, it's revealed that he's created such things as a meal contained in a stick of chewing gum, a teleporter, a glass elevator that works as a functional spacecraft, a youth serum in pill form and an aging serum counterpart, and so forth. Of course, not all of these things have been perfected yet, and some very interesting things have happened to both his test subjects and visitors to the factory who didn't heed his warnings...
The Fascination Lab and BeauTek seem to hire them by the batch. Though the latter is the "evil" company, FLab isn't afraid of exploring the potential of some freaky, questionable science. (They even have a literal Highly Questionable Tower, for Pete's sake.)
Common in Please Don't Tell My Parents I'm a Supervillain. Most super-intellects have difficulty controlling their power, since the human brain isn't designed to hold that kind of knowledge. This results in a number of impractical and downright stupid designs, such as putting a self-destruct on an otherwise perfectly normal smelter. The main character, Penny, is a mad scientist who's a bit better at this than most, and has invented technology strong enough to challenge adult heroes when she's only thirteen.
Captain Hasina is perpetually experimenting on people to test homemade cures, and when she learns Eric is an otherworlder, she becomes obbessed with cutting him open For Science!. Because these cures have innocuous side effects, and her Morality Chain prevents her from dissecting Eric, she's played for Comedic Sociopathy.
Nunnal Enaz is the Director of Hariana Inquires in the Hidden Elf Village of Dnnac Ledo. This means her day job is bending the laws of physics until they break in her laboratory. When Nolien mana mutates into a unicorn, she gleefully experiments upon him to learn about the new breed.
Tavarangian of The Stormlight Archive falls into this on his smart days. As a result of the Old Magic, his intelligence changes randomly from day to day, and his compassion and empathy change in inverse proportion to his intellect. So when he's smart, he becomes a psychopath.
In All Men of Genius, the numerous scientists of the cast aren't necessarily mad, but their output isn't necessarily much different than if they were, so a lot of the associated tropes apply. Some of them are certainly eccentric.
The Golgotha Series has Clay and Professor Zenith. Clay wishes to reanimate the dead, while Zenith wants to use humans as living batteries for his diabolical machines.
In the Erebus Sequence, this is revealed to be what the always-absent king has been getting up to. Among other things, it's the origin of the Orfani.
Starflight's father Mastermind from Wings of Fire is the chief scientist for the NightWings, dabbling in experiments and asking dragonets to help him out for their school projects. Because he had kidnapped RainWings to learn their defenses so his tribe could overpower them, he is arrested and sentenced by their new queen Glory to prison. Starflight finds it hard to trust his father after that.
Fifty Feet Of Trouble features mad scientists as a form of monster. The "scientist" part means they can make wonders. The "mad" part means they don't always make any sense. Like the giant glowing pigeons.
In Rogue Star, Cliff Hawk wants to know more about rogue stars—living stars which for whatever reason have not joined the intergalactic community of stars—and decides to build one from scratch in his own laboratory. It does not go well.