The Mad Thinker is both a mad probability expert, who can predict individual human behavior to a preposterous degree, and a robot master who constantly builds new robots and androids to sic on his enemies.
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.
A.I.M. (Advanced Idea Mechanics) is 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 very quickly turned against them).
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 his origin story for example:
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: Oh... what's that? Hank: 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!
His long-lost daughter Nadia van Dyne takes after him in terms of both brilliance (creating a pocket dimension lab at an age where pink crystal castles are the obvious go-to aesthetic) and obsessive tendencies (not having anything resembling a day/night cycle in said lab because anything indicating the passage of time is too distracting).
Ultimately deconstructed in both cases, as both father and daughter have been confirmed as suffering from rather serious bipolar disorder. Hank went undiagnosed for most of his adult life (with his periodic instability dismissed as eccentricity, an inferiority complex, or side effects of excess size-shifting) leading him to hit Rock Bottom several times. After Nadia's first major breakdown her friends and stepmother convinced her to get professional help and she is doing much better.
The High Evolutionary basically lives inside a Heel–Face Revolving Door. On a bad day, he's the quintessential Evilutionary Biologist, but even at his most benevolent, he's still got a towering god complex. His feats are danged impressive. Apart from creating his own race of Uplifted Animals called the New Men, he also built his own planet!
Blade's arch-enemy Deacon Frost was an amoral scientist who performed experiments to gain immortality; upon injecting himself with vampire blood, he becomes an unusual type of vampire with bizarre powers. He continued to perform his experiments such as producing clones of his victims (one of the special powers he gained), all so that he could usurp Dracula's position as Lord of the Vampires.
One of the villains of Ms. Marvel (2014), is a clone of Thomas Edison with the head of a bird called The Inventor. He is this in his own words, although not the kind "that's actually an idiot."
Dr. Rot from the Insane in the Brain storyline of Wolverine is a lunatic running an asylum, whose particular flavor 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.
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.
Rhona Burchill from Ultimate Fantastic Four was rejected from the Baxter Building Program for Gifted Children despite having the natural talents as a scientist, implicitly due to failing the psychiatric evaluation — since she went on to cut her brother's brain out and graft it to her own, justifiably so. As for what makes her mad... did you just read the previous sentence?
Bruce Banner usually isn’t this, but without the Hulk as an outlet, he can start to lose it as all his anger and darker impulses build up.
The Leader, who usually plays around with trying to take over the world, killing the Hulk, turning everyone into a Gamma Mutant and then trying to take over the world, or any combination thereof, a hideous mix of For Science! and For the Evulz.
