And they feel glorified doing it, cuz nobody ever calls them on it >_>
I think the most cruel would be Hojo, who ruined every single main character's life in one way or another, and thought he was doing good up until the very end. Lucrecia would also be up there, for what she did to poor Vincent.
Gestahl also strikes me as being particularly cruel for chaining up Celes, having guards beat her, pressumably killing Banon, faking remorse to trick the heroes, brainwashng soldiers, ordering the death's and draining of power f countless Espers, and other things.
One last mention, I found Tidus's completely pointless hatred of Jecht really cruel too. I mean, he hates him because his mom liked him? Weren't they married? Wouldn't it make SENSE for her to like him?
There's probably better examples, but I can't think right now.