The Mandarin is a Mad Scientist enemy of Iron Man. He spends his time inventing mind-controlling super-cancers that run around like a cross between the Blob and the Borg. Or inventing orbiting Hate Rays to destroy the world with madness.
Yes, some of his inventions were adaptations of said aliens' technology. Depending on the writers, the Mandarin has varying levels of superhuman martial arts, too, so he really is some kind of every-villain.
The Mandarin is Dr. Frankenstein and Remo Williams in one man.
Doctor Sivana and his family are similarly the archenemies of Captain Marvel and friends. He's a five-foot-tall gnome of a man with a chrome dome, huge Scary Shiny Glasses, and more often than not a white lab coat. His stated goals (in no particular order): To become Rightful Ruler of the Universe in fact as well as in name; to spread evil, cruelty, and nastiness throughout the cosmos; and to humiliate, discredit, and ultimately KILL CAPTAIN MARVEL! Heh heh heh heh!!! What, exactly, his incredibly attractive and affectionate late wife saw in him is a total enigma.
The original version of the character was actually a benevolent man who was ruined by being rejected by the scientific community for his ideas. When his wife died, he blamed the world and turned into the crackpot we love to hate. This was the Pre Crisis origin, the current version seems to always have been mean.
A heroic Mad Scientist in The DCU is Doctor Magnus, creator of the Metal Men.
In the Marvel Universe, AIM (Advanced Idea Mechanics) are a terrorist organization of Mad Scientists, who wish to overthrow the world's governments and institute a technocracy.
The Enclave is a similar group. Their most successful (or unsuccessful, depending on how you look at it) experiment created the being who would eventually become Adam Warlock (who eventually turned against them).
The DCU comic 52 had a secret conspiracy who was kidnapping Mad Scientists, good and evil, for a nefarious goal.
The Ultra-Humanite (arguably comics' first supervillain) who actually transferred his brain from the standard baldie-in-a-labcoat mad scientist's body into that of a beautiful woman. He was only another Mad Scientist in the Golden Age comics, but in the series The Golden Age, he becomes the arch villain, but poses as a hero and gets the medal of honor. He saved Hitler's brain, too. And put it in an invincible super-body.
D.A. Sinclair of Invincible is easily one of the most sadistic mad scientists in fiction. He started making zombielike techno-organic minions, Re-Animen, from dead bodies, which is bad enough. But he eventually moved on to live subjects, kidnapping his roommate and tearing out his vocal cords so that he couldn't scream while he operated on him (D. A. is a college student, after all, and can't afford anesthetic). And he tore his arm off and overrode his free will. Then he started duplicating the process on homeless people. Naturally, the US Government saw to it that he served no jail time when he was caught, and gave him a cushy job making Re-Animen for military use.
Dr Mindbender from G.I. Joe is particularly mad. Cloner, Genetic Engineer, Robot designer and master of mind control and inventor of many of Cobra's bizarre superweapons. That he's bald, usually shirtless and has pecs like melons only enhances his image of insanity. He even installed mind control chips in several prominent Cobra members, and prepared for his own death by creating a clone backup. Oh, and before he became a mad scientist, he was a... benevolent orthodontist. Until his freak orthodontics accident (seriously).
Simon von Simon from Little Gloomy. He's got it all, from his powerful machinery, futuristic inventions (such as the television and the microwave. Before you say anything, he invented them before anyone else did), hunchbacked Halfhearted Henchman, to his seething rage for everybody but himself. The fact that his plans for world domination were motivated by Gloomy dumping him, and the fact that the series calls him on not marketing his fantastic creations to get on top in a less freaky way undermines his menace somewhat; This, in turn, is offset by his army of ravenous zombies.
Dr Scyk from the Danish comic-strip "Dr Merling".
Several villains in the Blake and Mortimer comics fall under this trope. The most notable being:
Wade/Jonathan Septimusin "The Yellow M"
Miloch Georgevich in "Sos Météores" and "Le Piege Diabolique"
Voronov in "La Machination Voronov". Who also ends up being something of a Karma Houdini.
In Y: The Last Man geneticist Dr Allison Mann claims she was illegally cloning a nephew who needed a bone transplant. She later admits this story was fictional to gain Agent 355's sympathy rather than be thought of as a 'mad scientist'; her actual motive was to spite her father who was nearing success in cloning the first human. After several red herrings we encounter the REAL mad scientist is in fact Allison's father, who was seeking to clone his daughter so he could be a better parent the next time round, yet who also sabotaged Allison's cloning experiment out of sheer spite and may have accidentally caused the plague that all but wiped out all males.
In addition to Dr. Robotnik/Eggman, the Archie Sonic the Hedgehog comic has Dr. Finitevus and Dimitri, both of whom work for the Dark Legion, a group who believe in self-augmentation with technology.
Hank Pym (a.k.a. Ant-Man a.k.a. Giant-Man a.k.a. Goliath a.k.a. Yellowjacket a.k.a. The Wasp). Just take for example his origin story:
Panel of Scientists: You should stick to practical projects. Hank Pym: No! I'll work only on things that appeal to my imagination... like my latest invention. Panel of Scientists: Oh... what's that? Hank Pym: I won't tell you yet! You would only laugh at me as you've done before! But when I've finished it, I'll show you! Then you shall know I'm a greater scientist than any of you!
Marvel's High Evolutionary. The man built his own planet!
Mr. Freeze used to be one of these, with no real backstory, just the whole freezing schtick. Then came Batman: The Animated Series which gave him chillingly tragic backstory and motivation, turning him more into a villainous Woobie. This new version of the character was Retconned into the main DCU.
Barry Ween, the 10-year-old with a 4-digit IQ in the eponymous series The Adventures of Barry Ween, Boy Genius. A representative quote: "Hey — put that down! That's the controls to my weather satellite! You just flooded Norway!" [short pause] "Well... it's only Norway..."
Batman rogue Scarecrow is an expert psychologist who creates fear gas that preys on the target's most deeply seeded phobias.
Krona (of JLA-Avengers fame) is a mad scientist from a species of humanoids who had discovered immortality and realized the potential of the mind's raw power well before Earth's solar system had formed. He was determined to unlock the secret of existence: How had the universe come into being? To this end, he created a "time window" that would allow him to peer at the moment of creation. Unfortunately, apparently the act of looking caused the creation to go awry, and instead of a single universe, a multiverse was formed. Unfortunately, this included one evil antimatter universe... and the seeds for the Crisis on Infinite Earths were sown. Krona was banished, but eventually was employed by Nekron (the Lord of the Unliving) and turned into the embodiment of entropy. As such, he gradually grew in power, until he reached a point where he vivisected entire universes in his restless quest for answers. He forcibly interrogated Galactus to find out what he knew. All in the name of science.
It can be hard to tell — Blackhawk seems to feature gadgetry unbelievably ludicrous enough to fall under mad science in every issue, and frequently right on the cover.
Dr Rot from the Insane in the Brain storyline of the Wolverine comic, a lunatic running an asylum, whose particular flavour of insane science is psychic machines made out of human brains. Adequately summed up by the following quote, while he flees Wolvie with a fresh brain in one hand and a handful of cables in the other:
Even better, he pulls it off. By the time Wolvie catches up with him, he's turned the brain into a psychic grenade that drives everyone else insane for thirty seconds so he can escape. He uses a slightly-different set of improvised components, sadly.
The Awesome Slapstick had Dr. Denton, Destroyer of Worlds, a five-year-old genius who built a giant robotic teddy bear.
There is a double subversion in Universal War One. The scientist who invented the wormhole is the only one to care about a possible Time Paradox, so he kills the fools who want to 'go home' even if it endangers the universe. However, when Kalish explains to him there is no way to create a time paradox, the scientist becomes mad.
Samantha Argus of Safe Havens is a personable, enthusiastic grad student who has unlocked the genetic code. She has the power to transform practically any living creature.
German comic Nick Knatterton once had Professor Bartap, who invents a shaving foam which is also a very effective explosive. Unintentionally. (Comedic version, definitely.)
Hugo Strange from Batman is an archetypal mad scientist. He's an expert in everything from chemistry and genetics to psychology, and uses it for evil.
The Military Doctor in Sturmtruppen: He believes he's discovered the Invisibility Elixir without getting insane, while his attendants point out that's actually the other way around. He also thought that a case of anemia was actually caused by a Vampire.
Warren Ellis's Doktor Sleepless intentionally invokes this: nobody listens to "real people," so he becomes the cartoony mad scientist character of Doktor Sleepless to draw attention.
Runaways: Chase's parents, Victor and Janet Stein are a pair of these.
Transformers: All Hail Megatron makes Brainstorm into one. He seemingly has no qualms about putting suggestion ideas inside Kup's mind at Prowl's request to exert more control over the army. In Transformers: Last Stand of the Wreckers Brainstorm works at the Kimia Facility, an R & D lab full of mad scientists. And Brainstorm in particular is considered especially insane even by their standards. He makes a hobby of creating weapons so horrible, they're classified as unmentionable by the Ethics Committee. In Transformers: More than Meets the Eye he builds all sorts of weapons and a holding cell for the crew and to hold Overlord, including a gun designed to shrink people, a bomb designed to break the fourth wall, and a overpowered laser gun labelled My First Blaster (complete with flashing lights and sounds). Tellingly, when someone asks him about one of his inventions snuffing out a sun, he dismisses it as "filthy, stinking lies"... because they got a small detail wrong.
Also from Wreckers is Ironfist, whose weapons have been responsible for the death of millions of cons, but he himself is quite naive and doesn't know of their effects as well as the war's toll outside of statistics. He builds a gun which targets the brain, and that was banned by the ethics committee.
Skyfall is a less comedic and naive example; he isn't as smart or successful as the others, but he's quite mad, and sold Ironfist's most deadly invention to the Decepticons, and rigged one of those brain bullets to lodge inside Ironfist's skull and kill him.
Everett Ducklair, the creator of One and many of the gadgets Paperinik uses, is a unwilling case: because of his Science-Related Memetic Disorder, he simply can't create something without turning it in a weapon. He eventually retreats to a monastery to meditate and search for the better part of himself.
In the reboot "Pikappa" we have Vendor who is much less concerned about creating dangerous inventions.
The Weapon X project in its entirety is built on the backs of mad scientists, experimenting on mutants to create powerful and deadly weapons.
Its civilian offshoot, the Facility, carries on the practice. Dr. Sarah Kinney's proposal to clone Wolverine, when mainstream science had only just begun having success with sheep and cats, is initially considered outright absurd by Zander Rice (though it owed as much to Rice's hatred of Wolverine for killing his father). Kinney outright equates cloning a mutant with godhood.