Dr. Weil is notable in being one of the most evil beings in the Mega Man series despite only appearing in a few games. Following the peaceful resolution of the Maverick Wars by the sentient superprogram, the Mother Elf, Weil decided that Reploids needed to pay for their crimes. To this end, Weil corrupted Mother Elf by turning her into the Dark Elf, and triggered the Elf Wars. Weil used the Dark Elf and her children, the Baby Elves, to control Reploids and force them to fight each other in massive battles, which resulted in the deaths of 90% of all Reploids and 60% of all humans. Defeated, exiled and transferred into a mechanical body for his crimes, Weil eventually returned one hundred years later, consumed with a thirst for vengeance directed at all life for the perceived crimes against him. Weaseling his way into becoming the supreme ruler of Neo Arcadia, Weil turns it into a dystopian hellhole. When he breaks his citizens to the point where they're desperate enough to risk escaping into the wastelands to form their own colony, Weil decides to obliterate their new home with a Kill Sat. When his Kill Sat is disabled, Weil attempts to drop it upon the colony, killing everyone in the region. Cruel, megalomaniacal and displaying an unprecedented level of sadism in the series, Weil reveled in the suffering of others and desired nothing less than to make human and reploid alike feel like their existences were living deaths.
Gemini, from the first game, kills one of his allies for no reason when he could've easily helped her and defeated Mega Man. He also manipulates a boy with multiple personality disorder into helping him to blow up the entire planet and is revealed as the one who manipulated King Cepheus into destroying the AM Planet.
Mr. King is the leader of the organization, Dealer, and the Big Bad of the third game. Appearing to all the world as a benevolant millionaire who donates to chairty, in reality Mr. King is a Manipulative Bastard willing to use anyone for his own benefit. As the operator of Joker, all of Joker's crimes lead right back to King. In addition to forcing his own Wizard to self-destruct to defeat his enemies, King adopted orphans and forced them to undertake suicidal missions in order to further his own plans. In fact, it is said that Jack and Tia were the only orphans to survive these missions. He then proceeded to take control of Meteor G so he could take over the world by force, raining down deadly Noise upon those who would not subjugate themselves to him. However, after being betrayed by his subordinates, King who was supposedly destroyed, became an Energy Being and decided to wipe out the world using Meteor G because he figures that if he can't rule the world, he will destroy it.
Dr. Regal is a Card-Carrying Villain and the leader of the organization known as Nebula. To prove his belief that Humans Are Bastards, Regal has his organization devoted to converting the world to evil by causing wars and spreading as much misery as possible. He subjects Lan's father to horrifying Cold-Blooded Torture and gleefully turns innocent NetNavis into servants of evil, slowly corrupting the whole Net. His end game is to connect the souls of everyone in the world to Nebula Gray, a program he created from the darkest thoughts of people, and corrupt the entire planet. At the end of the fifth game his father, Lord Wily, the notorious leader of a cyberterrorist organization, pulls an Even Evil Has Standards moment and subjects him to Laser-Guided Amnesia to destroy his evil personality and force him to reform.
Anime-only character Slur, The Dragon to Big Bad Duo, is both a Knight Templarand a Complete Monster. Slur is fanatically devoted to exterminating all evil from the universe...where by "evil", she means everyone who doesn't agree with her master's extremely draconian concept of morality. In other words, Slur wants to kill all humans just because she doesn't like us. And unlike Duo, Slur has no sense of fair play - she deliberately "sabotages" the Humanity on Trial plot of Stream by giving Asteroid Navis to evil people, so that Duo will be convinced that Earth doesn't deserve to live. Vicious, sadistic, and with no redeeming qualities at all, Slur might very well be the vilest Battle Network villainess ever.
Dr. Wily attempted to send the moon out of its orbit to kill off most of humanity, forcing the survivors (if there were any) to consider him king, so he could prove he was better than Dr. Light. He's also tried to use earthquakes to destroy cities, threatening to destroy them if they don't obey, and he's tortured Mega Man mentally twice in the show, first by making him wonder if he's just a mistake created by Dr. Light, the second time making Proto Man be a Heel Face Mole- even Proto Man considered this act wrong during the plan-and ordered him to kill Mega Man after this.