Well Chruser, Shishio is the villain of the show's main plotline, but he is a great character.

Dark, brooding and very intelligent. Heck, his "special fighting techiques" are actually cheating. (He has a oil soaked blade that creates flames when it strikes and a glove coated with gunpoweder that he explodes in an enemy's face.)

I thought he was one of the best villains ever in a show.