101 Dalmatians: The Series: P.H. De Vil, Cruella's cousin who she often collaborates with to carry out some of her schemes. He's usually inventing some kind of device to accomplish some evil deed, such as an earthquake machine, a personality splitter, and a robotic version of Rolly. He is also willing to test dangerous chemicals on animals without any consideration of the harm he may be doing to them.
Adventure Time: Princess Bubblegum is the sweet, benevolent ruler of the Candy Kingdom, but is also a highly intelligent scientist. Although normally level-headed and innocently sweet, she has created two zombie plagues, created a giant immortal candy sphinx who almost destroyed the kingdom, created a screaming nutcase who threatened her with his own sword, has skeletons chained to her walls, created a potion that can permanently paralyze someone, killed a jellyfish to make a sandwich, tried to have the Duke of Nuts killed, and tortured the Ice King. Her "For SCIENCE!" attitude, and her devotion to the law, cause... interesting things to happen. Assuming that he was the one who designed and built the Reconditioning Chamber and the Sound Sword, then Lemongrab definitely qualifies.
The Alvin Show has Clyde Crashcup, who tries (but always fails) to "invent" something.
The Dark Knight always seemed to be neck-deep in mad scientists on Batman: The Animated Series. Within the first five episodes of the show, he runs afoul of Man-Bat, The Scarecrow, and Poison Ivy, scientists-turned-supercriminals all. Scarecrow actually goes the whole hog with the trope, as his initial appearance features a plot to ruin the university he was fired from and murder all those who called his sanity into question. Which should answer the question of his sanity quite comprehensively.
Joker:Beneath this puckish exterior lies the mind of a genius years ahead of my time. In the weeks young Robinwas undermy tutelage, I used him as the subject of my greatest experiment. Using cutting-edge genetics technology which I pinched here and there, I encoded my DNA in a microchip and set it in Bird Boy's birdbrain.
Tarantulus of Transformers: Beast Wars is, if not a mad inventor, certainly crazy enough and scientific enough and treacherous enough to qualify for Mad Scientist.
This is actually a case of Character Development; in the first season, while he was the Predacon Science Officer, he was characterized more as "that creepy bot who'll eat anything he can catch". This was Adaptation Displacement—in the original toylines, he was a (still cannibalistic) ninja warrior.
The Beatles have come across a couple of mad scientists. Professor Psycho (from "Baby's In Black") brings a vampire girl to life and tries to get her married to Paul, while Dr. Dora Florahyde ("If I Fell") wants to transfer John's thoughts into her Frankenstein's Monster to bring it to life. (This was unintended as the doc told The Igor to get the brains of a beetle. Igor responded that John is "the brains of the Beatles.")
The original 1993 series has Dr. Karbunkle, who often creates inventions for Limburger and his minions to use against the Biker Mice and also experimented on the Biker Mice, which resulted in Modo getting an eye-patch and a robotic arm and Throttle being blinded and needing special sunglasses to see.
The 2006 Sequel Series has Dr. Catorkian, a Catatonian scientist who creates inventions to help the Catatonians and Ronaldo Rump defeat the Biker Mice.
It's all but stated that her insanity is the result of brain damage from the accident that scarred her. It's a pity that the only character in the show who had healing powers (Gaia, that is) was the one Blight would never be willing to go to for help. Just remember the times when she tried to kill or at least harm the Spirit of Earth.
Code Lyoko: Franz Hopper is less "mad" than he is "slightly unhinged". Still, though, he manages to create a computer program that can venture into the world, take people hostage, create poisonous gas, create blizzards, and many many other things, so he definitely counts.
Darkwing Duck: Megavolt. Likewise Bushroot, who's usually ignored in this capacity, because his "mad science" is botany.
The Dick Tracy Show has the Brow and Oodles in possession of Dr. Von Stooker's notebook which has a formula to turn people invisible ("Lab Grab"). Joe Jitsu plants a phony book on the crooks, with the resulting mixtures they make turning into Gargle Blaster stuff.
Futurama: Professor Farnsworth takes this to the lengths of parody and beyond, casually creating doomsday devices, atomic supermen and hybrid lifeforms, experimenting on himself, and being several forks short of a silverware drawer.
He builds Doomsday Devices a lot. Oh, he doesn't plan to use them, he just seems to think they're cool. "I suppose I could part with one and still be feared..."
At one point the Planet Express crew were figuring how to enter New New York's Central Bureaucracy.
Prof. Farnsworth: You can't just waltz into the Central Bureaucracy! It's a tangled web of red tape and regulations. I've never been, but a friend of mine went completely mad trying to find the washroom there. Leela: Then we'll need a guide, someone who's been there before. Prof. Farnsworth: Oh, I've been there. Lots of times! (Laughs maniacally)
One episode revealed that he spent twenty-five years in a mental institution starting when he was a teenager. His rival and former student, Professor WERNSTROM! is of the evil (or at least asshole) variation.
Garfield and Friends: One builds the Incredibly Stupid Swamp Monster. How madis he?" asks Roy. "He's so mad," replies Orson, "he spent ten years trying to cure his pet cat's measles before realizing it was a leopard."
Gargoyles: Dr. Sevarius isn't quite mad so much as he is amoral, but he displays a touch of the theatricality that is the hallmark of the best nutty professors.
Generator Rex: Cesar single-handedly invents weaponry that can take down an entire highly-trained government base, but is a Cloud Cuckoo Lander on a good day and a totally lacks any sense of practicality or ethics on a bad day.
"I'm not MAD! I'm Dr. Focus!" (gets arrested) "Now I'm really mad!"
The 1999 feature film has Dr. Artemis Bradford and his daughter, Brenda, both of whom designed the title cyborg. The 2003 sequel has Baxter, who could possibly qualify...
Invader Zim: The title character is a mad scientist himself. In fact, in a script for an incomplete Start of Darkness episode about him, Zim was actually a military scientist for his race whose creation, an "Infinite Absorbing Blob" was responsible for killing two of his previous leaders.
Dib and Professor Membrane would arguably qualify as Mad Scientists. Dib perhaps more so since his inventions revolve around his all-consuming obsession to destroy ZIM, whereas his father's inventions are more geared toward helping humanity. Even the Super Toast.
Heloise isn't the only one in Miseryville (the town even has an award ceremony just for them). One recurring character is Dr. Ludwig Von Scientist, a German-accented evil genius of a demon who's got more forehead than body. He's usually just the go-to "evil scientist" character when Heloise isn't available, but in "Heads Will Roll" he's shown to be Heloise's arch-rival and the only one who comes somewhat close to being as good of a mad scientist as her.
Johnny Test's older sisters Susan and Mary are both Mad Scientist teenagers. Also their friendly enemy, Eugene, a.k.a. "Bling Bling Boy".
The Legend of Korra: Varrick, although he's less cacklingly crazy and evil and more quirky and amoral.
Mega Babies: Nurse Lazlo. A much earlier example is Dr. XXX, the title character of the 1933 short, The Mad Doctor.
Milton the Monster: Professor Weirdo and Count Kook create a monster with six drops of essence of terror and five drops of sinister sauce. Professor Weirdo means to add a tincture of tenderness so the creation would not turn on him, but Count Kook accidentally knocks in the entire beaker. The creation becomes the childlike Milton.
My Life as a Teenage Robot: Most of Tremortons citizens think that Nora Wakeman is this. While she is more saner then most of the examples listed, some of her inventions dont seem to serve a true purpose.
My Little Pony 'n Friends: The gizmonks, from "The Great Rainbow Caper", are obsessed with invention and experimentation for their own sake, gleefully cobbling together complex machines for no real reason or gain, and sometimes without even knowing what they're supposed to do.
Dr. Doofenshmirtz is an Affably EvilPunch-Clock Villain trying to conquer the Tri-State Area. He insists on being called an evil scientist, considering "mad scientist" a slur. His alter ego from the 2nd dimension was one, but now serves as the dictator.
With Phineastein, the Regurgitator, Professor Poofenplotz and all the members of L.O.V.E.M.U.F.F.I.N., it seems the show runs on this trope.
The Brain of Pinky and the Brain always devises a scheme to take over the world, several of them involving machines and potions. He quite often pilots mechanical bodies to appear human and once tried to hypnotize everyone by feeding them pancakes laced with hypnotic fluid.
PJ Masks: Romeo, a Child Prodigy with a knack for creating evil inventions and planning to take over the world.
Mojo Jojo, complete with evil laugh. Also, he's a monkey.
Professor Utonium, although he's far more benign than most. Every time he creates something useful (including the Girls themselves), it's by accident. But when he tries to do something intentionally, it leads to a disaster.
Rick Sanchez from Rick and Morty is as mad as they come, though he replaces the usual creepiness and cackle-happy lunacy with heaps and heaps of apathy for everything and everyone else (except maybe his grandchildren Morty and Summer and his daughter Beth). He's someone who gives absolutely zero fucks about leaving his entire dimension to die, and fleeing into another where his counterpart had died half a minute ago, burying him in the back yard and taking over his life, and that makes him just as crazy as the cackling lunatic the trope usually conjures.
Velma Dinkley, the brains of the Scooby gang, becomes a mad scientist in the DVD feature Scooby-Doo: Frankencreepy, but only because she was hypnotized.
In the classic episode "A Gaggle Of Galloping Ghosts," Shaggy and Scooby play "mad scientist," whipping up a formula that would turn werewolves into pussycats. It is summarily rejected.
Scooby himself becomes one in The 13 Ghosts of Scooby-Doo episode "That's Monstertainment" when he and his pals are zapped into an old monster movie.
Scooby: Rive my reation rife!!
Parodied by Sheep in the Big City's Angry Scientist (who becomes especially angry whenever anyone incorrectly refers to him as a mad scientist).
The Simpsons: Professor Frink is a rather more amicable Mad Scientist, always apologetic when things go wrong with his inventions, and has a passion for inventing crazy things like self-aware robots that only scrub floors, auto-diallers with retractable wheels, automatic tap-dancing shoes, buildings that can sprout legs and run away from danger, and hamburger earmuffs.
Frink:(as a radio controlled baby-plane with his son in it crashes) Oh dear. My wife is going to kill me.
Skysurfer Strike ForceBig Bad, Cybron who creates at least seven (maybe his own daughter too makes eight) lethal cyborgs, then wires an experimental computer brain into himself.
Dr. Bent, a.k.a. Overlord in Spiral Zone, a particulary nasty one for a kid's show as he created a horrible mist that causes "zones" that turn people into mindless zombies.
On Spliced, almost all of the characters are the creations of "some crazy doctor" based on Dr. Moreau, who was arrested prior to the series by authorities disgusted with the freaks of nature he created.
Dr. Nuvo Vindi was a former medical doctor who disappeared sometime around the Battle of Naboo before resurfacing in the employ of the Separatists. With their backing he decided to resurrect the Blue Shadow Virus, a plague that no known species is immune to and killed many people back in the day. Vindi went a step further to make it deadlier by converting it from a water-based strain to an airborne strain and having it delivered via bombs on key Republic worlds. After he's captured and his assistant droid sets off all the bombs in his hidden bunker, he's excited at the idea of one of the battle droids exiting the bunker and releasing the plague across Naboo.
Not of the cacklingly crazy variety, the Techno Union has been shown to dabble in inhumane experiments on sentient beings in both this show and the now Legendsmicroseries. In the Bad Batch arc in this series, Wat Tambor has the previously thought dead Clone Trooper Echo plugged into a stasis tube to be used as an organic computer against the army he fought for, while reliving the moment of his "death" on loop for months. They also built the Organic Decimator, a small weapon that seeks out organic matter and vaporizes it, which in the unfinished reels, Tambor casually tests on a captive native as a threat to intruders. In the latter series, they kidnap male Nelvaanians and mutate them into brainwashed, cyborg supersoldiers. While the latter series is not canon, the Techno Union's activities on Nelvaan have been re-canonized.
The first Superman short, "The Mad Scientist," has one as the villain, threatening to enact vengeance on all those who laughed at him with his electrothanasia-ray.
Transformers Animated has Prometheus Black. He started out messing around with biochemical enhancements to try and beat out Professor Sumdac's robotics industry, but after a lab accident changed him into the supervillain Meltdown he went into full vengeful mad science mode. The chemical warfare specialist Oil Slick might also count, although outside the fact that he's a ninja who developed the Transformer equivalent of ebola not much is known about him.
Animated! Blackarachnia also has elements of this. The Allspark Almanac reveals she invented triple-changing, and her attempts to better understand her techno-organic mutation lead her to try and create another hybrid...resulting in Waspinator.
Wheeljack of Transformers: Generation 1 is one. Part of his appeal was him convincing the other Autobots that his crackpot inventions were worth something.
His Shattered Glass counterpart is also a mad scientist, but less the cheery genial type normal Wheeljack is, and much, much more pure distilled ranting They Called Me Mad! type of mad scientist.
Dr. Arkeville from the G1 cartoon. Though his madness was one upped by Starscream himself in Countdown to Extinction.
Simon Bar Sinister, the main antagonist on Underdog, a short, nasty-looking scientist only about two feet tall, who's goal was to Take Over the World. Unlike most examples of this trope, he tended to actually listen when his henchman Cad Lackey made suggestions.
Dr. Thadeus "Rusty" Venture on The Venture Bros., although his lack of ambitions and laziness mean that he comes up with far fewer superweapons and far more get-rich-quick schemes than most of his ilk. Other M.S.'s in the Ventureverse include Pete White and Master Billy Quizboy, Jonas Venture Jr., Otaku Senzuri from the lost pilot, Professor Impossible, Mike Sorayama, Dr. Septapus, Baron Ünderbheit (implied), and Phantom Limb (implied confirmed, as part of his backstory)
Wallace from Wallace & Gromit is an eccentric Absent-Minded Professor, although he usually uses his inventions for mundane things such as window-washing and humanely rounding up bunnies so they don't get in the way of the town's upcoming vegetable-growing competition. This has resulting in one case of mind-switching, Wallace turning into a Were-Rabbit, a penguin attempting to use his inventions for a jewel heist, and Wallace nearly getting killed several times. Luckily, his dog Gromit is loyal to a fault, an acepilot, and smart enough to be able to fix things whenever they go wrong (and they do, frequently).