Kenshin outlives two children, has two more and two grandchildren taken out of this world for their own protection, and has to watch his final grandson fall to evil and insanity. He comes to believe he’s fated to lose his children.
In a moment of insanity, believing that he is doing the right thing, Kenshin starts peeling Aoshi's skin off and almost kills him. The only way that could have been worse for Kenshin's mind is if it had been one of his children.
Yukito has hir babies taken away forever, pulled directly from hir arms, for their own protection.
Saitou dies alone in his old age, a widower with all of his family save one adopted son driven away by his own distantness, and his lovers too busy* albeit busy trying to fight fate and save him to stay with him.
Saitou also gets called to a location to find his Morality Pet, a sweet and innocent doll girl with a mental age of about six who he’s all but adopted, shielding another little girl and being stabbed by the adults that were supposed to take care of her. It’s probably no wonder he immediately moves her in with them where he doesn’t have to trust anyone else to protect her.
Aoshi was involved with Saitou before being turned by and involved with Kenshin, yet he is slowly but surely forgotten by Saitou as Saitou turns into a kami. He’ll spend his time on phone calls asking about the Kaibas’ welfare and never mention Aoshi at all; he can’t even remember his name. Even when he comes back he doesn’t seem to notice him. Aoshi and Kenshin originally think it’s some form of dementia, but that just asks the question, which is worse: (being immortal and) watching your loved one slowly deteriorate, or having your loved one lose interest in your relationship and not even tell you?
Similarly, after the apocalypse they’re all leaving each other behind. Kenshin is meditating in a lava pool where Aoshi can’t even touch him for ten years, Saitou is an ancestor kami who no longer needs to sleep and has half his attention always on his clan, and when Aoshi evolves into a chaos demon he spends less than half his time with them and doesn’t bother to sleep there. They all know they’re growing apart and can’t do much about it.
Inuyasha lives in a town populated by his descendants, whom he calls “grandkids”, and when they start going mad and attacking people, he’s the one who has to kill them.
Saitou is kept alive far, far past the point of death by what was supposed to be a blessing while he is tortured and experimented upon by Kurama. Aoshi determines after he is rescued that he is alive even though he has no heart.
All of Kurama's victims in general; he has one alive with her organs suspended like fruit from one of his evil trees.
Atem enjoys this... He utterly destroys the mind of Kenji's killer from the inside out. Later, when he is slipping into insanity, he reveals to Seth that he has several people he is absolutely mind controlling, letting them experience only what he wants them to, though they seem so normal from the outside they can still keep their positions as guards.
Aoshi essentially mind-crushes Seto - he implants his own memories of Hell into him and then leaves him there trapped in them, his body in a coma, for five months.
Atem and Seth's treatment of Rei, a mentally unbalanced and later vulnerable teenager, would cross the line into torture for anyone sane. Several other characters even have some trouble with the Questionable Consent aspects of the relationship themselves.
Ryou after the apocalypse, uses his power to force rapists to continue having sex with him until they die, even when they're begging for it to stop.
Saitou won't actually confirm it, but he hints around at the fact that for more than a year he was tortured in prison by constantly being raped. He doesn't specify whether it was just the guards or other prisoners as well.
And worse yet, he was forced to enjoy it instead of fighting by Bakura's curse on him.
Bakura's curse on Saitou wouldn't be a walk in the park anyway - he's mentally controlled into responding to anyone's sexual interest with lust, and be submissive unless otherwise ordered. No matter who it is or how he feels about them.
Ryou drains rapists to death, and then keeps their souls as ghosts helplessly bound to him. The reason this isn't a case of Pay Evil unto Evil? Because Ryou doesn't realize he's doing evil. He calls them his "friends".