Dartz from the DOMA arc reached his Moral Event Horizon when he started killing off the protagonists, but the most horrifying example and crossing of his MEH is when the identities of the Mirror soldiers are revealed to be everyone's favorite characters: Joey, Mai, Yugi, and Pegasus. From then on, he used them as frickin' HUMAN SHIELDS. This was a true Kick the Dog moment to not only the remaining protagonists, but the entire fanbase as well; a few children are said to have broken down crying because of this act.
After this, it is revealed that he retroactively crossed his MEH before either of the above, when he caused the deaths of Alister and Raphael's loved ones so that he could induce anger in their hearts and manipulate them into joining DOMA, disguising himself as Gozaburo in the case of the former.
Pegasus, in the manga. While he is just as tragic as his anime counterpart, he lost the sympathy of several manga readers when he telekinetically forced Bandit Keith to commit suicide, and would have fully crossed the line if Bandit Keith wasn't an Asshole Victim who was threatening Pegasus with a knife moments before. The anime changed this to simply having Keith dumped into the sea in a classic No One Could Survive That!, which he does.
His treatment of the Kaiba brothers might have already put him over the line: he has the kidnapped Mokuba's soul stolen... and when Kaiba and Yugi (plus Yugi's friends) reach for him, he taunts Kaiba by showing the Card where Mokuba's spirit was stored, then had Mokuba's Empty Shell of a body bring him his deck. And then he defeated Kaiba (while cheating with his Millenium Eye) and de-souled him! Even Yugi, who isn't one of Kaiba's biggest fans anyway, was all "This Is Unforgivable!"
Another from the manga is the entire Death-T arc for Seto Kaiba. From hiring a Serial Killer who exclusively kills children to abandoning his brother Mokuba, ostensibly his Morality Pet, to die, it's no wonder Yugi punished him by shattering his soul to pieces and rebuilding it from scratch; the later, Anti Heroic Kaiba who would be more familiar to those who saw the anime first is thus arguably a completely different person.
Dark Marik immediately crossed the horizon when he tried to stab his foster brother Odion in his sleep, and then proceeded to lay down a brutal, psyche-damaging Mind Rape to Mai in their duel.
Dark Bakura crossed the line with his plan to resurrect Zorc into the mortal world in the final arc, hoping to kill everyone and cast the entire world into darkness and destruction.
Others Series
Yu-Gi-Oh! 5Ds: Rudger, leader of the Dark Signers, crosses it when he abandons his duel with Yusei and forces Rally, who's like an adopted little brother to Yusei, to fight in his stead. The fact that Rudger takes glee in Rally's intentional loss (which led to his death) and Yusei's anguished reaction only drives the knife further.
