Wall of text incoming. Maybe not all of these are villains that I really just hate in the same way as you’re asking, but these are some people I think did some of the most heinous things in Doctor Who. Leaving out any of the big ones like Davros, the Master, etc.
Bennett - The Rescue: Probably not a common one to list, but this guy killed a whole crew of a ship, including the father of a child who he kept alive so he could manipulate her into believing his twisted version of events, and attempted genocide of the Dido people to cover up his crimes. Truly one of the most despicable people in Doctor Who.
El Akir - The Crusade: Just a vile, sadistic person. The one who told Barbara “the only pleasure left for you is death. And death is very far away.”
Salamander and Benik - The Enemy of the World: The first is just a cruel dictator, with no end to his tyranny, and he keeps a whole secret bunker of innocent people hostage to aid in his plans. Benik takes so much pleasure in just being a cruel person.
The War Lord - The War Games: The idea of just abducting soldiers from Earth’s historical wars to build an army to take over the universe is truly obscene. He deserved every moment of suffering the Time Lords gave him.
Captain Dent - Colony in Space: There are few Who villains that have been as uncaring about the people they have to make suffer in the name of their own profits than Dent.
The Marshal and Jaeger - The Mutants: Imperialists that want to take over already owned land is bad enough, but to try to completely convert the atmosphere of the planet so that it’s uninhabitable by the native people is another level.
Hilda Winters and the Scientific Reform Society - Robot: Maybe this one is because the techno-fascist ideas these people have in this one is becoming less and less far-fetched, but they are all truly nasty people.
Nyder - Genesis of the Daleks: He knows how bad Davros and his plan are, and yet he’s faithful to the end. It doesn’t bother him in the slightest what Davros does to their own people, what he wants them to become. He might even be worse than Davros.
Harrison Chase - The Seeds of Doom: There’s appreciation for plant life, and the reasonable concern over what man is doing to his own planet, and then there’s this guy. He legitimately believes in plant superiority to the point that he wants to eradicate all animal life for the plants. Also the whole putting people through a chipper-shredder to turn them into fertilizer thing.
Castellan Kelner - The Invasion of Time: By no means the main villain of the story, but he’s such a pushover, so willing to bend over backwards for whoever wants to oppress his own people to save his own skin, a traitor of the worst kind, and I think worthy of mention.
Queen Xanxia - The Pirate Planet: Taking their own planet, and materializing it around other planets, destroying their entire populations in order to get all of its mineral wealth buried into Zanak. The Captain did the actions, but under the direct control of Xanxia, who is using vast amounts of the energy of Zanak to keep herself alive and put her consciousness into a hologram to continue the obscenity.
Lady Cranleigh - Black Orchid: Keeps her son locked up in a room when what he really needs is medical and psychiatric help, and lets him kill people in his insanity while covering those crimes up. She even walks away from this with no consequences. I don’t think people talk enough about how bad she is.
Morgus - The Caves of Androzani: Sharaz Jek may be horrible, but let’s not forget the reason he became the way he did, to get revenge on his former business partner Morgus, the one who ruined his entire life for financial gain. Pretty much the grandfather of all evil businessmen in Doctor Who, looking out for no one but himself and his profits, will let anyone die or be severely hurt in the process.
Shockeye of the Quawncing Grig - The Two Doctors: Honestly this guy and his gluttony for food, and desire to eat even beings as intelligent as humans, cannibalistic tendencies, Shockeye is just disgusting.
The Slitheen Family - Aliens of London/World War Three, Boom Town: Destroying an entire occupied planet just to turn it into fuel you can sell to the highest bidder, and then trying to destroy Cardiff to escape and get away with your crimes. All pretty terrible when you think of it.
The Family of Blood - Human Nature/The Family of Blood: So dead set on their quest for immortality that they’d stop at nothing to get it. It would have been the town, then the UK, then Europe and beyond if the Doctor didn’t come back and trick them. I’m not sure when the death toll would have stopped if they were allowed to keep going until they eventually died.
Max Capricorn - Voyage of the Damned: a bit of a comedy villain, but he was going to basically nuke a planet as part of an insurance fraud and insider trading scheme. That’s pretty terrible.
Mr. Halpen, Commander Kess, and Solana Mercurio - Planet of the Ood: I think running a slave company is enough said. Halpen because he’s in charge, Kess is particularly sadistic with how he treats the Ood and how he goes a bit crazy in a game of claw, and Solana because she was so close to a chance at some redemption until she doubled down and sold out the ones trying to save the Ood to the guards.
Hawthorne The Government of Starship UK - The Beast Below: Constant torture of an innocent creature, the last of its kind, that wanted to do nothing but help save humanity.
Kazran and by extension Elliot Sardick - A Christmas Carol: Kazran (at the beginning, before the Doctor changed him) had the power to save a ship full of people but chooses not to because he simply doesn’t care. Elliot was the equally horrible and abusive father that turned him into this.
Madame Kovarian - Series 6: A recurring villain but abducting a pregnant woman to turn her baby into a sleeper agent to kill the Doctor, one of the mother’s closest friends, and take away her ability to raise her own child, even for the sake of preventing the return of the Time War is completely despicable. I don’t think Amy should feel guilty for what she did in the abandoned timeline.
Solomon - Dinosaurs on a Spaceship: Just a truly terrible person with no redeeming qualities. Sees everything only in terms of financial value, and sees people as property. I’m fine with the Doctor letting this guy die.
Kahler Jex - A Town Called Mercy: A war criminal, pure and simple. His helping of that town to try and make up for that doesn’t change that fact. I’m with the Doctor, it’s not up to him to decide how his own debt to society should be paid.
There are probably more, but I’m struggling to come up with more from the 12-15 eras. There seems to be less focus on truly terrible people individual villains over the last while on the show, or what I can think of is a Master, or a Rassilon, or a Tecteun, the kind of names I am excluding from such a list.
Not strictly a villain but I find Andred unforgivable for the Gallifrey audios >:((((
