The manga and second anime series, Brotherhood, has some surefire examples:
There's Shou Tucker, a Mad Scientist who transforms his own daughter into a Half-Human Hybrid, partly to see if he can and partly to retain his State Alchemist status. He had previously done the same thing to his wife. He's the only character who even comes close to triggering Al's Berserk Button, and what he did leaves a stain on the Elric brothers' memories for the rest of their lives.
Just to put things in perspective: of all the characters who died in the story (shortly after Tucker's arrest, Anti-HeroScar breaks into his house and bloodily murders him), he's the only one who was sent to Hell in the "In Memoriam" omakes. The authoress Hiromu Arakawa allowed even characters like Envy or Kimblee to get to Heaven, because she thought there was still something worth saving about them. With Shou Tucker, she was absolutely merciless, and with good reason.
Even after he's died, it gets even worse. Later on, it turns out that what he did was totally and completely pointless because the military already had much better chimeras. Imagine straight up humans who can harness the instincts of a specific animal and even turn into that animal temporarily in order to fight better, like the Lizard with none of the Superpowered Evil Side effects. Compare that to the paralyzed husks of pain that became the Tucker family.
The Big Bad, Father, is often seen as one, sacrificing entire nations to achieve A God Am I status. But is so alien that it's hard to tell.
The alienness of Father seems to stem from the fact that it surrendered its "sins" to sacrifice its human-like qualities and create the homunculi. When it destroyed Xerses, it had much more of a personality...and that was the personality of a sadistic monster, smiling maniacally all the time, especially when the country was being destroyed and Father temporarily Ascended to a Higher Plane of Existence.
Zolf J. Kimbley is an odd example. On the one hand, he's a Sociopathic Soldier who sees killing as a job, Loves the Sound of Screaming, and enjoys demolishing entire city blocks with his explosions. He sees no moral difference between saving lives as a doctor and taking them as a soldier and is willing to side with the homunculi just to see how the conflict is going to turn out. On the other hand, he's also deeply self-aware of his own psychopathy, loathes hypocrisy, and is a major believer in human potential. Kimblee essentially straddles the line between CM and Even Evil Has Standards—he does have a code of conduct and a sense of right and wrong, but it's a code that no human being would ever see as moral.
The unnamed and utterly heinous Dr. Goldtoothnearly kills Riza by slitting her throat to force Roy to cross the Gate, spends every second onscreen crossing the Moral Event Horizon, and otherwise is essentially Tucker 2.0.
From the Brotherhood movie, we have Security Chief Atlas, who killed the movie's female protagonist's parents, then stole her brother Ashley's skin, and used it as a disguise in order to trick the rebel group, Bats, into making a Transmutation circle for him in order to gain power to rival other nations. He also stabbed the guy who was secretly in on this as well because he needed more sacrificial blood. He gets his comeuppance when a Philosopher's Stone-empowered Julia and Ashley, who turned out to have survived the ripping of his skin via Philosopher Stone and work up the ranks to become a commander of the Creta military, kill him in the end.
Mugear wanted to introduce a toxic chemical into pregnant women to produce an alchemical amplifier. Before that, he had no problems producing said amplifier at the cost of the villagers' health. He also murdered Nash Tringham, the inventor of the method, after he refused to use the method or continue the research on it due to the health risks for the people of his village and tried to sabotage its use by Mugear.
Brigadier General Basque Grand (a Reasonable Authority Figure in the manga) is portrayed as a sadistic Colonel Kilgore and one of the key players in the Ishbalan massacre, who laughed maniacally as he gunned scores of civilians down with his Philosopher's Stone, authorizing its use in order to turn the massacre into a massacre. Grand forced Roy Mustang to kill Winry's parents because they were treating Ishabalan patients, even though they were also treating Amestrian soldiers. When he discovers what Shou Tucker had done to his daughter, he decides to cart her away for study, presumably so he could bully Tucker into making more chimeras lest he lose his State Alchemist license. When Scar blows his brains out, it is very, very satisfying.
The Big Bad, Dante, is an obvious one. She manipulates and abuses her homunculi servants and sends them to their deaths if they don't do exactly what she wants. Their desire to become human leads them to question if she really intends to make them human (she doesn't), and she can't have that. She plots the destruction of an entire nation in the hopes that it will convince someone to create a Philosopher's Stone, which she can then steal in order to live a few years longer (when she's already Really 700 Years Old). And that's on top of already being a body-snatching bitch who plans to hijack the body of Rose, who already went through serious Break the Cutie, including Rape as Drama and Teen Pregnancy.
