Ghetsis, definitely. He just holds so much power and seems to be on an unmatched level of evil. Also, he has an alluring and immensely memorable design. He is cold, calculated, and indignant, whilst being well-rounded and still maintaining humanness. Ghetsis is everything a villain should be.
Cyrus would be my second choice. Perhaps this is because I saw a lot of him in the anime and thought he was also quite a dynamic character. I think the anime truly made him multi-dimensional and I've always been intrigued by his desire for the creation of a new world. I think he is a very interesting individual overall and a minuscule part of me perhaps feels somewhat sympathetic towards him.