Hojo is a frigging crazy SOB and a sicko at the same time. He gets over shadowed by Shinra's wrong doings and Sephiroth, but left to his own devices he definitely had the ability to mess up peoples lives. Perhaps on a smaller scale, but what he did to Lucrecia is pretty damn awful.
Sephiroth is also cruel. Manipulating Cloud and seemingly enjoying his struggling and pain, at times even laughing at him. But originally, he was actually a pretty 'okay' guy... maybe.
However, I think Shinra would take my pick. Mainly because all the problems stemmed from them. The fact that President Shinra would just watch an entire sector collapse and kill hundreds, if not thousands of people. Forces his ideas on other nations/towns/places. Puts people in danger for the benefit of his own wallet, and if they survive, kills 'em anyway. Would definitely be on Santa's naughty list.
But great, he dies. Oh, crap, he has a son... who is even more of a lunatic. At least according to his introduction. Yay, for family!
So yeah, Shinra get's my vote.