Organized by the various worlds, in order of main series release, here's the worst of the worst in the Final Fantasy series.
The main series
Final Fantasy IV
In Final Fantasy IV, depraved Mad Scientist Doctor Lugae proves to be the template for monstrous scientists in the series, who transformed Edge's parents into chimerae, as well as gleefully altered his composition into a monster himself. His actions disgusted his superior, Noble Demon Rubicante, to the point where the latter had to explain to the party he was just as offended as them with Lugae. Remarkably, he has himself very little screen time, but he nonetheless makes very good use of it.
The true monster villain of the game is Zemus. He was the only voice pushing for world domination among the Lunarians, same bloodline as Cecil and Golbez/Theodor. Zemus was forced by his own people to fall into a millennium-long coma to allow humanity to evolve until the two could coexist peacfully together. Even in this state, he is still capable of manipulating Golbez to carry out his unsettlingly extreme dreams of an all-Lunarian utopia, which involves not only committing the atrocities throughout the entire game, but also using the artificialabomination Giant of Babil capable of dealing massive amounts of racially-based genocide on a global scale. Besides Golbez, Zemus also manipulates Kain during his fight with Cecil, who has turned into a paladin. It is also strongly implied that Zemus was responsible for the brainwashing of the four essences' incarnations, thus being responsible for the atrocities committed by the Elemental Fiends.
Final Fantasy VI
Kefka Palazzo's backstory establishes that he was the first Magitek knight created, but the imperfections of the process drove him insane. It shows through the various acts he performs throughout the game including arson, poisoning Doma (made more impactful by showing how it affects the character of Cyan, whose wife and son die in the process), stabbing General Leo to death after the latter tries to stop him, killing the Espers at Thamasa (not caring about the deaths of the Magitek-armored minions accompanying him) and destroying the world halfway through the game. He seeks joy in destruction and is prone to laughing like mad amidst the chaos. He has also stated that he enjoys hearing people scream. Kefka absorbs the magic from the Warring Triad, so when he is finally defeated all of the magic disappears from the world and all the espers go extinct. While some of his dialogue is darkly comicalnote In the American localizations, changes due to translation can make Kefka appear charmingly affable at times to many people, more so in the SNES version than in the GBA version, his actions are portrayed in a horrific and often tragic light. He embodies despair, hatred and death and believes that life is meaningless, finding destruction fun because "precious lives" are lost. His personality and, to a lesser extent, his appearance is best summed up as the Final Fantasy -equivalent of The Joker. Dissidia: Final Fantasy shows Kefka in a bit different, extremely narcissistic light, evidenced when the player fights a mirror Kefka. "Oh, who's THAT handsome devil?!" He is also made more tragic a figure by the statement having his heart broken is a part-explanation for his insanity and that he can't express his emotions in any other way than laughing. He also elaborates on his philosophy of destruction: "Why create, when it will only be destroyed? Why cling to life, knowing that you have to die? None of it will have meant anything once you do!"
Final Fantasy VII
Professor Hojo, the Mad Scientist from Final Fantasy VII, may not be the primary antagonist, but he is responsible for nearly everything bad happening in the game. Prior to the game proper, he injects Jenova cells into the womb of his wife, Lucrecia, in order to turn their son Sephiroth into a supersoldier. He later murders Aerith's father and experiments on both her and her mother, his research leading to the latter's death. Throughout the game he is implied to manipulate most, if not all, of Sephiroth's actions, because he thinks of Sephiroth as research he wants to see blossom. He tries to mate Aerith and Red XIII, experiments on the survivors of the Nibelheim massacre, murders Vincent, experiments on him and attempts to help his son destroy the world at the end of the game.]] It was also implied that Hojo was the one, who wrecked one of the mako generators at the Nibelheim Reactor to lure Sephiroth to the reactor and receive his first clue about his possible origins before Crisis Core placed the implications of Genesis doing this act. Dirge of Cerberus reveals Hojo to have copied his mind into the body of an experimental supersoldier and used him to order other experimental supersoldiers to commit mass kidnappings and murders, with the ultimate goal of awakening Omega and fusing with it. Hojo can basically be summed up as the Final Fantasy equivalent of Dr. Josef Mengele.
Fuhito, in one of the prequels, acts scientist for the original AVALANCHE. His mindset can be described in a single expression: Hojo's his hero. In addition to that, Hojo likes him a lot enough to seriously consider leaving Shinra to work with the guy. Fuhito found a way to copy part of Shinra's SOLDIER program. With the data he invents his own variant complete with monstrous degradation of the mind and turning the subject into monsters. He takes two of the SOLDIERs Zack later remembers and turns them into abominations on par with Hojo's aberrations. He later finds an ancient Ultimate Summon that has been broken long, long ago. He implants a piece in an innocent girl, transforming her into a weapon to be AVALANCHE's spearhead against Shinra, while the piece starts sucking out her life to rebuild itself. He establishes a firm powerbase to release the Summon, which is to burn the entirety of the world. In the end, he winds up taking it all and merging with it. We all know what happens when you do that.
World of Ivalice (includes Final Fantasy XII and Final Fantasy Tactics)
Several antagonists in the story at least have some sympathetic qualities, but not so for Folmarv Tengille, who is responsible for all of the bloodshed in the conflict just to revive the fallen Ultima, an abusive father, who murdered his own son and massacred an entire castle, kidnapping Alma so that he could use her as a host body for Ultima. At this point, he's already one of the most despicable characters in the game. Then he decides to resurrect the recently deceased Zalbaag and force himto fight Ramza as a Player Punch.
Dycedarg Beolve turns out to be one. He murdered his own father for power and, along with his childhood friend, Duke Bestrald Larg, plunged Ivalice into civil war against Duke Goltanna. Then he backstabs Larg as well, and when his brothers Zalbaag and Ramza call him out on his actions, he has the audacity to be offended. When he merged with Adrammalech, he murdered Zalbaag as well. This all arguably makes him worse than Folmarv/Vormav, who might not have initially been a CM.
Final Fantasy XII features Judge Bergan, who decides, on a whim, to slaughter half the population of Mt. Bur-Omisace, including Gran Kiltias, who was the in-game equivalent to The Pope. He enjoys killing anyone who would stand between him and his goals, including his ally, Judge Drace. His ultimate goal is to dominate everything with sheer physical might, no matter what happens to anyone else.
Dissidia: Final Fantasy
Shinryu from Dissidia: Final Fantasy willingly turns Chaos into a Nigh Invulnerable, Ax-Crazy force of destruction, knowing full well that this will likely destroy the world he's supposed to be watching over, purely out of spite. Scenario 000 reveals that pretty much everything in the Dissidia series is entirely his fault. To wit, he takes advantage of Cid's grief and rage over his wife's death and tricks him into a Faustian deal under the guise that he would help make Chaos strong enough to defeat the nation of Onrac. Instead, however, Shinryu strips Cid of his body so he can never die and thus forever witness the cycle of death, creates Cosmos as a direct mockery of Cid's wife and keeps the War going for untold centuries, all to increase his own power by draining the warriors from both sides of their memories at the end of each cycle. Sometimes he doesn't revive one of the warriors and instead leaves their spirits to rot in the Void for eternity simply because they no longer have any strength for him to steal.
Crystal Chronicles series
Larkeicus is an immortal Clavat from Final Fantasy Crystal Chronicles: Echoes of Time and a nasty piece of work. Originally, his goals were for the good of humanity, since he invented special crystal powered inventions to give the people of the world untold riches. Once the crystals began vanishing, though, the citizens blamed the collapse of the world on Larkeicus. They found a crystal in the forest and at first, Larkeicus wanted to investigate it. He instead had a change of heart and killed the villagers in the village near the forest, which disgusted his apprentice Veriaulde the Yuke. Veriaulde tried to stop his master, but was knocked out. Sherlotta, the only survivor of the massacre, was a prime target of Larkeicus as she was given the ability to spawn crystals. Larkeicus decided to capture her and experiment on her and his apprentice For Science! so he could obtain immortality and be treated like a god again. Because of his master's experiments, Veriaulde transformed into a monster on contact with any crystals, which was a boon for Larkeicus, who wasn't concerned with the Yuke's well being at all. Throughout the game, Larkeicus is shown to have free agency and is perfectly able to stop what he's doing, but is too engrossed in the scientific experiments he is conducting to really care about his apprentice or anyone else.