One Piece makes occasional mention of the Gorousei's Evil Genius, Dr. Vegapunk. He is one of the most speculated-upon characters in the manga. Apparently, he's a pioneer in the fields of robotics and Devil fruits, having created a cyborg with Devil fruit powers (Kuma), multiple copies of said cyborg armed with laser weaponry, and figured out a way for inanimate objects to "eat" Devil fruits.
To a lesser extent, Gecko Moria's right hand man Dr Hogback, a surgeon of legendary skill who assisted Moria in creating a zombie army.
John Smith (no, that's not an alias) from Mai-Otome, with a dash of Mad Scientist thrown in.
Princess Kycilia Zabi, the Lady of War from Mobile Suit Gundam who also was the Zabi family member in charge of Newtype research.
Shader in Chrono Crusade serves as the Sinner's main techie. Aion, the Big Bad, has elements as this as well, considering he's a bit of a chessmaster.
Herr Doktor in Hellsing is the evil genius for Millennium.
Hakase in Mahou Sensei Negima! probably would have played this part in Chao's evil army if not for the fact that Chao was also an Evil Genius of an even higher degree. Still, this was essentially her role in that she was the one overseeing the ritual to remove the world's Weirdness Censor, not actually taking part in the battle.
Of course, whether either of them actually qualifies asevil is up for debate.
In Gundam SEED, Nicol, The Dark Chick, also took on this role to the Antivillainous Le Creuset team, relying on stealth, caution and an Invisibility Cloak. It only made him more of an outcast on a team of guys who wouldn't know subtle if it bit them in the ass. One could argue that Big Bad Rau Le Creuset also plays this role.
In Gundam Wing, Chief EngineerTsubarov was this to the Romefeller Foundation. A brilliant technician, he invented the remote-controlled Mobile Dolls whose useage consumes much of the subsequent plot; he's also one of the few men at the OZ base who realises that using the captive Gundam pilots as test subjects might be a bad idea. Curiously, he had a personality that one would more typically associate with The Brute being a thuggish Jerkass and Smug Snake who loathed pacifism, had No Indoor Voice, dealt with problems by applying as much brute force as possible, and went out in the midst of a truly epic Villainous Breakdown, ranting about how he was invincible.
Alister/Amalda was this to Dartz's group of henchmen in Yu-Gi-Oh!. Nesbitt plays this role to the Big 5, being their tech guy and weapons expert; oddly enough, he's perhaps their poorest duelist.
The Cyborg Superman builds all of the technology used by the Sinestro Corps, including the Manhunter robots who recharge yellow rings and the space station they used as a base.
Darth Maladi from Star Wars Legacy is both a Sith alchemist and the head of Sith Intelligence. She's generally portrayed as one of the most cunning Sith characters in the comic, but seems to enjoy her schemes and experiments more for their own sake than from the hope of doing anything constructive with them.
Also Vul Isen as he is believed to be a scientist. He never accepts anything without a proof.
In All Fall Down, IQ is VERY bitter about not being one of these anymore.
There are occasional subversions: Whitaker, Khan, Kananga, Drax, Kristatos, and Le Chiffre were all the "main brains" in their operations as well as the leaders, and Sanchez had what is nearly a parody of one named Milton Krest. Stromberg has two, both of whom he kills early in the film to cover his tracks.
Grand Moff Tarkin from Star Wars could count, as he has the Death Star, and is a strategist with his own doctrine.
And in the prequel trilogy era, Nute Gunray and the Seperatist Council fit the role as they the brain of everything, and later when they are no longer needed, they are killed by their boss.
James McCullen and The Doctor in G.I. Joe: The Rise of Cobra. At the end of the film, the Doctor becomes the Big Bad, Cobra Commander, and turns McCullen into Destro.
Mystery Men's Casanova Frankenstein is an evil Disco genius. Even his archnemesis asks him for help with his quips. He wears a set of golden finger cuffs that carry sonic rays and hyper-lasers, and a pair of slippers that emit poison gas. And that's just what his enemy knows he's wearing while he just sits around in his dressing gown.
In A Fistful of Dollars, Ramon Rojo is a non-stereotypical example. In a family of archetypal Mexican banditos, Ramon is The Strategist, concocting the plan to steal the gold from under the Mexican army's nose, and orchestrating the eventual massacre of the rival Baxter family. He's also the only one to see through Joe, and keeps a wary eye on him throughout the film, eventually deducing that he is the traitor in their ranks.
In The Witcher, we have Vilgefortz. He is easily the most smart and powerful wizard in the North, and he let it get into his head.
Tyrion Lannister from A Song of Ice and Fire, an educated, smart, and calculating dwarf sort of qualifies. However, he wasn't really an ally of House Lannister and he was enemies with Tywin. He embodies this trope in his own organization, in which he is also the Big Bad. He isn't really that evil though.
The Artemis Fowl series is full of these, which makes sense, since the protagonist himself is a Teen Genius, and that requires antagonists to match. We have Artemis himself in book 1 (in his status as Villain Protagonist), Opal Koboi in book 2, Jon Spiro in book 3, Opal Koboi again in book 4, Minerva in book 5, Opal Koboi AGAIN in book 6. Turnball Root in book 7.
The Star Wars Expanded Universe gives us Bevel Lemelisk, chief designer of the Death Star, although the actual designers were superintelligent alien children whose planet was being held hostage.
Most incarnations of Power Rangers and Super Sentai have one of these among the villains, with responsibilities commonly including mass-producing Mooks and the Monster of the Week, making monsters grow, and generally being the one who knows the most about the finer points of the magic/technology of the season. In Power Rangers, the first and probably the most iconic among fans was Finister, the series' first monster maker.
Elizabeth from Wicked Science becomes a genius and she uses her new intelligence as a way to try to get money, fame and Toby's affections. The evil part is that she has little morals when it comes to use her inventions, including using a teleporter to sneak in Toby's laboratory so her goon can destroy/steal/sabotage whatever Toby is creating in the episode, or trapping him in a Groundhog Day Loop so he accepts the new universe in which he's trapped, where they are a couple and his friends hate him.
In Magic: The Gathering, it could be argued that Yawgmoth is this, but in New Phyrexia, with its five-color theme, Jin-Gitaxis, the blue praetor, takes this role.
Professor Hojo in Final Fantasy VII is this to President Shinra. After Shinra is killed, Hojo either remains the Evil Genius or gets promoted to Big Bad, depending on which side of the multi-faceted "who's responsible for Sephiroth's actions" debate you're on.
Or Sephiroth remains the Big Bad that he always was (as confirmed by Word Of God) and Hojo was demoted to a mere Mad Scientist.
In Advance Wars Black Hole Rising and Dual Strike, Perky Goth Lash provides the bad guys with all of their advanced technology.
Caulder/Dr Stolos in Days of Ruin, who eventually becomes the Big Bad.
Hazama/Terumi Yuuki from BlazBlue. The most dangerous thing about his genius, however, isn't his trancendental knowledge of alchemy, which allowed him to create the titular Blaz Blue, the Black Beast, Arakune and some other unpleasant things, but rather his tactical genius, which, so far, has allowed him to outmaneuver an omniscient supercomputer with three minds (although he had help with the guy below). Then again, Hazama himself would qualify in any positions given in the Five-Bad Band.
If this is what Hazama entails, then there must also be a mention of Relius Clover, a brilliant researcher who sought only perfection and has performed horrendous experiments and are also capable of various Xanatos Gambit (as shown during his EX Story where he practically played Sector Seven and Kokonoe for chumps to create his Ignis, still accounting his Implacable Man status). He just got less time to shine than Hazama though his inclusion as a playable character and a story mode for him in Extend might elevate him.
Although one could equally argue that he's the Dragon, as he appears to be the only member of the Order beyond Sanctus who truly understands what's going on, killing him is the last thing that needs to be done before the final confrontation, and the nominal Dragon is a Honor Before ReasonHero Antagonist.
Dr. Elvin Atombender from the Impossible Mission games is a genius computer programmer and former university professor. Although he has been unstable his whole life, he officially became criminally insane when a power failure caused the deletion of an artificial intelligence program that he had nearly finished. The player must stop him from hacking into the defense networks of the world's superpowers and starting a nuclear holocaust.
"If I win, I get to be a king. If I lose, I get to be a legend."
Please that's just Genre Savvy. His real genius shines in is his military and political capabilities. He was able to conquer eleven nations in 8 months before he was forced out by a coalition of twenty-six other countries. Then after that he crafted a plan that would get him and his adventuring group into ruling the whole continent by controlling multiple nations through figureheads in a scheme that eventually would absorb the whole continent while still making it look like there are three different empires remaining.
Wayward Sons: Doctor Chu, who very much enjoys performing torturous experiments on live subjects.
The Global Guardians PBEM Universe has several. Doctor Simian, the Evil Mastermind, Brainchild, and Baron Malthus are the most notable examples.
In the Whateley Universe, there are lots of Mad Scientist types. The ones who work for other supervillains tend to be characters like Chessmaster or Nimbus. The two of them nearly destroyed Whateley Academy on Halloween.
Doctor Octopus goes the extra mile by having "Evil Genius" printed on the side of his coffee mug in The Spectacular Spider Man. Although he is subordinate to no one.
