He still was a bastard in Space Seed. A megalomaniac who used others for his own ends. That's pretty evil in my eyes. But, playing devil's advocate... he kind of had a reason to be angry in Wrath... his wife got killed on the planet... and Kirk and co... had left them there.I think for "cruelty" champion, I pick Trelane. He seem to delight in it, for no reason but his own pleasure.
Dr. Adams is in the running.
Captain Tracey and Kor were certainly ruthless, but I didn't get the impression they enjoyed it, but I guess that doesn't make them less cruel.
I wouldn't pick Space Seed Khan, but Wrathful Khan, yes.
I think the Salt Sucker was a cruel beast.
Actually, one of my favorite things about Star Trek is the lack of "villainous" villains. A lot conflict is because of cultural differences and misunderstandings rather than what things devolve to in the time of the Star Trek movies.
In a way though, I figure they rose up and struck back against him.