Bishop Ladja from Dragon Quest V, despite only being The Dragon, becomes one of the vilest characters in the series in the DS remake. He specializes in committing an even more horrific atrocity than his last in most of his appearances. His first scene alone has him brutally beating the hero and Harry (who are six years old at the time) to within an inch of their lives, laughing sadistically all the while. Then, when the hero's father, Pankraz, arrives to save the day, he threatens to murder the hero if Pankraz tries to fight back against his enforcers. After the enforcers are done beating him, Ladja coldly finishes off the dying Pankraz with a giant fireball, then carts the hero and Harry off to a brutal slave labor camp for over ten years. He's also at least somewhat successful at being The Starscream, killing off one person ahead of him (King Korol) in the chain of command for the power. Finally, he makes sure to wait until the main character reunites with his mother (after over 18 years apart) to kill said mother, just for maximum emotional impact.
Mortamor, the Big Bad of Dragon Quest VI, most definitely counts. Unlike the other Dragon Quest villains, Mortamor doesn't simply want to destroy/conquer the world. No, he wants to completely and utterly destroy the very concept of hope. To this end, he effectively turns his own world, which he rules, into a giant concentration camp where his subjects are routinely abused, manipulated, tortured, and slaughtered like animals. Those few who manage to resist his soul-crushing ways are instead shipped off to a special prison where they are starved, tortured, and ultimately executed hundreds at a time. One sample act to show how he goes about destroying the spirits of people is manipulating an entire town to kill each other over a treasure chest he planted in an elderly woman's house. Possibly the worst part is that Mortamor wasn't satisfied even after the slaughter. No, instead, he rewinds time to right before the massacre and starts the whole thing over again. The people of Greedmore, until the party's intervention, have been unknowingly trapped in an endless cycle of deceit, death, and rebirth, all because Mortamor loves watching his subjects suffer.
Rhapthorne from Dragon Quest VIII is one of the most repulsive villains in the series. While the characters aren't initially aware of it, Rhapthorne is present from the beginning to the end, actively causing all the calamities in the game. His most heinous acts include turning the residents of the castle Trodian into immobile plant people, killing the kind old woman in cold blood (after forcing her to come out by holding her son hostage), and ordering the murder of an unborn child of the Godbird Empryea. He also did most of his work by performing Grand Theft Me, which trapped the victims of that into mental torture.