Yami Marik, a split personality off of the original Marik. Born out of Marik's pain and hatred towards his fate as a tombkeeper, Yami Marik is brutal, depraved and sadistic without end. The first thing he does upon his original creation/release is kill Marik's father brutally by skinning him alive with a bronze knife within the Millennium Rod, then immediately try to do the same to Marik's only friend, Rishid. When he got loose again during the finals of Battle City, he imprisoned Mai and the real Marik within labyrinths of their own loneliness (and in Mai's case, this is after severelymind-raping her in their duel), attempted to murder Rishid several times, nearly killed Marik's older sister Isis, was knowingly roasting people with attacks from the Winged Dragon of Ra and set up a shadow game meant to actually kill the loser. His deck is even based on torture devices.
Yami Bakura, the evil alter ego of Bakura, who is the reincarnation of an Egyptian bandit who fought the Pharaoh/Yami Yugi. His first acts included attempting to kill/send Yugi and his friends to the Shadow Realm in order to possess the Millennium Puzzle. He loses, but comes back soon after to try to use Mokuba as a new host until Tristan saves him. In Battle City, he enters the competition by sadistically sending three Duelists to hell/Shadow Realm. In the final season, he goes from recurring antagonist to Big Bad and tries to unleash the dark god Zorc upon the world, with the intent of killing or enslaving everyone.
Brron, Mad King of the Dark World, is one even though he's only in a few episodes. He kidnaps Judai's friends and plays a card that kills them/sends them to the stars in front of him, eventually bringing out a Woobie, Destroyer of Worlds Judai/Jaden
Divine/Sayer. When we see him duel Rua/Leo for the first time, and how cruelly he dealt with Carly, we see that he's a jerk. Then he gets worse.Turns out, only did he torture Misty's younger brother to death in a series of extremely dubious "tests" and try to turn Aki into a Woobie, Destroyer of Worlds, he framed poor Aki for the former and LAUGHED ABOUT IT. He is the most monstrous villain in 5D's, a series that thrives on the Well-Intentioned Extremist theme. He gets a very satisfying Karmic Death when Misty decides to let her Earthbound Immortaleat him alive.
Lotten on the other hand, is a tyrant lording over a small western style town called Crash Town, who forces those he's defeated to join him or face slavery in the mines. Once he does get into an inconclusive match with Yusei, he actually sets up dynamite to kill them in the resulting cave-in, including an innocent child. Unsatisfied with the lack of slaves, he forces his own men to duel for their own freedom, which is stopped by Yusei and Kiryu. Once he does start to lose, he and his sister, Barb attempt to throw the duel and run away, but not before he abandons the manipulative bitch of a sister, Barb to her fate and setting off explosives in the town. Thankfully, Kiryu beats him and sends him to prison.
Tron, Freudian Excuse aside, has become one of these. Between what he does to Haruto, Droite, Kaito, and IV (His own Son.) It's pretty hard to sympathize with him. He also has III, his other son, make Yuma undergo a Despair Event Horizon. However, it turns out that the Barian World made the kind Bryon into the cruel Tron.
Vector himself also qualifies, seeing how he gleefully manipulated Faker into almost destroying all of existence by using the latter's love for his sons. In addition to this, in episode 94, he destroys several buildings and puts peoples lives in jeopardy JUST to get Yuma's attention.
Then there's how he lured Yuma to Sargasso using his good "friend" Rei as a hostage...only to reveal he had been playing Yuma like a fiddle during their duel, basically rearranging Yuma's deck with impunity...as Rei. He essentially tore Yuma's trust to shreds, and even used a card called Vain - Sneer of Betrayal that almost resulted in Yuma decking out by taking advantage of those new V cards he had given Yuma as Rei, had a horrifying Nightmare Face while showing his true self, and even gloated over it and distorting Rei's catch phrase just to screw with Yuma. Aside from defeating him while he possessed Faker, there was absolutely no reason for Vector to go to such extreme, disgusting lengths to destroy Yuma in such an emotional and psychological manner. Even his fellow Barians seem disgusted with him or unwilling to work with him.