In Final Fantasy II, after the party fails to stop the Dreadnought's completion, your next visit to several of the game's towns will be met with craters, damaged buildings, and NPCs mourning the loss of friends and family. This is when it becomes clear that the Emperor isn't kidding around, and he only goes farther from there.
Kefka is introduced as more of a nuisance, but a general of the enemy Empire nonetheless. His clownish charm fades rather quickly, however, after he disobeys direct orders and poisons Doma's water supply. The situation up to that point: General Leo had Doma Castle besieged, and was likely to win in just a matter of time with minimal casualties. Some time after Kefka arrives, Leo is summoned back to Vector to meet with the Emperor. Now there's no one to stop Kefka from dumping deadly poison into the Doma River, killing absolutely everyone in the castle; men, women, children, and Imperial P.O.W.'s that he knew full well were still trapped inside. The kicker here, which cements this act as Kefka gleefully tapdancing and cackling his way across the Moral Event Horizon, is that the Empire was going to win anyway. There was absolutely no possible justification for this heinous war crime other than Kefka wanting to hear "the music of hundreds of voices screaming in unison".
His only excuse at all for all this? As an early magitek knight, the process very likely drove him insane. No, that doesn't cut it.
Emperor Gestahl, while not nearly as crazy as his subordinate Kefka, still crosses the line when he is shown in a flashback to have orchestrated an invasion of the Esper world. While the invasion ends in failure, at the end he discovers an infant half-esper, and rips the baby from her mother's arms, killing the woman in the process, while gloating about how he's going to subject her to a life of experimentation. Oh BOY.
Note that in the original SNES translation of the game, this is somewhat softened; Madonna actually asks Gestahl to take care of Terra (which doesn't explain the thwack he still gives her afterwards, however). This was most likely due to Nintendo's Never Say "Die" policy at the time rather than a change or error on Ted Woolsey's part.
Of course, the Wham Episode of the game, when Kefka causes a cataclysm when he intentionally moves the statues out of sync on the Floating Continent, more than cements his status as not only an evil person, but a usurpingBig Bad, as well.
Sephiroth in Final Fantasy VII is initially shown to be quite sympathetic despite Cloud's hatred of him. He saves the party at Shinra HQ and seems to be working against the Evil Corporation finding the Promised Land. Even during Cloud's flashback, when you discover that he's not human (his Mom, Jenova, is actually a feminine alien in a tank), he remains worthy of pity. But then he goes crazy and burns down Cloud's hometown, killing Cloud's mom and Tifa's dad among others, as well as almost killing the devastated Tifa when she lost it and tried to take revenge for her father. And if that wasn't enough of an Event Horizon for you and you're still somewhat willing to feel sorry for him, there's always the part where he murders Aerith.
President Shinra and Heidegger ordering the destruction of a sector of Midgar just to get rid of some terrorists. The Turks (mainly Reno and Tseng) might have crossed the line too by actually carrying out this heinous order.
Then there's Scarlet leading mass murder via the complete destruction of the town of Coral.
And Hojo. Where do we start with Hojo? Injecting alien cells into his unborn child? Murdering Professor Gast right in front of his wife Ifalna and his child Aerith, whom he then kidnaps for horrible experiments? Doing more horrific experiments on Vincent, Zack, and Cloud? Also being indirectly responsible for Sephiroth's descent into insanity as well as Sephiroth's aforementioned murder of Aerith? You might as well assume that he crossed the line right at very beginning of his career. Taking the Expanded Universe into account, Hojo's life seems to consist of finding new lines to cross and gleefully leaping over them like he was practicing for the long jump.
Judge Bergan's rampage on Mt Bur-Omisace in Final Fantasy XII, in which Imperial troops murder unarmed refugees, their guards, and priests indiscriminately, and follow up by killing the Gran Kiltias Anastasis. Putting Bergan down like a rabid dog immediately after finding out is very satisfying.
Final Fantasy XV gives us Ardyn Izunia. Most of the characters only see this character as a creepy one, but not one they consider a Big Bad. That is, until he stabs Lunafreya when she's at her weakest when trying to reason with Leviathan in Altissia, the other characters helpless to do anything about it.
Final Fantasy Tactics has the despised Algus Sadalfus, who at first appears to merely be a classist Jerkass until he casually kills Tetra when an enemy tried to use her as a Human Shield.
Gerrith Barrington from the same game is far worse, he razes Rapha and Marach's village and kidnaps them to raise for the purpose of using them to claim the Throne of Ivalice for himself. If that doesn't push him into irredeemable evil territory, his sexual abuse of Rapha definitely does. He's essentially the Ghetsis Harmonia of Final Fantasy, only worse.
Ansem (actually Xehanort) definitely crossed this line in the original Kingdom Hearts when it was revealed that he experimented on living people just For Science!. And it was outright stated that the experiments caused their hearts to collapse! In this series, hearts are a Captain Ersatz for souls. So essentially, his experiments caused people's frickin' souls to collapse!
Master Xehanort may have did a lot of bad things throughout his life, but extracting the Darkness from Ventus's heart and creating Vantias (which almost led to the boy's death) really says a lot. But he may have already crossed it in his youth, when he travels into the future and destroys Sora's heart. Or earlier, when he almost suffocates the boy.
Saïx of Organization XIII crosses this when he coldly refuses to take Sora to Kairi, opting to use her kidnapping to make the Keybearer full of rage if it means collecting more Hearts to finish Kingdom Hearts for, what Saïx wouldn't know at the time, Xehanort's ultimate goal of using it to make clones of himself.
Multiple Disney Villains have crossed the line, but the moment they crossed it is often the same as in their source films. This is not the case with Jafar, Lady Tremaine and her daughters, Scar, and Clu; all of them have committed acts so heinous that they're viewed as larger monsters in this franchise than they are in their films.
Jafar crosses this line when he orders Genie to show him the Keyhole for Agrabah. Had Sora not shown up, the end result of this would amount to genocide, as the world would've been destroyed by the Heartless, and everyone in it being killed, which is what Jafar wanted. He is far worse in Kingdom Hearts II, where he becomes an Omnicidal Maniac bent on destroying the entire universe.
Lady Tremaine crosses the line when she outright tries to murder Cinderella with an Unversed which was summoned from her hatred towards her. Her daughters cross the line with her at the same time.
Clu crosses the line when he forces Sora to fightTron/Rinzler, then kills the latter after the battle.
However, all of this amounts nothing to the actions committed by Maleficent throughout the entire franchise. She's single-handedly responsible for hundreds, if not thousands of worlds being destroyed, and the deaths of billions of innocent people; a record unmatched in Disney history until the Starkiller Base. She's kidnapped girls who's hearts are pure light and forced them into deep sleep until all seven of them are brought together for universal domination (or worse, the end of reality itself). And she's even tricked Terra into stealing Princess Aurora's heart, and is in direct league with Xehanort.
Scar might be operating on a smaller scale than Maleficent, but he still manages to be far worse. Aside from his canon atrocities, he crosses the line when he gleefully tries to eat Sora shortly after the later arrives in his world. What makes this particularly vile is Sora is in the form of a Lion Cub, so Scar essentially wants to cannibalize a child. It's also worth mentioning that he's the only character in the series so far other than Xehanort that's been able to keep his original form as a Heartless.