A villain can be from a side character to a protagonist of the story, the minimum requirement being the "dark energy" he/she has is bigger than his/her "bright energy".
E.g. Although Light Yagami is the protagonist, you can consider from his homicidal acts that he is a villain.
My favorite villain is Johan Liebert from Monster:
Reasons:
He has an IQ of at least 150.
He is a sociopath and caused 50 people to kill each other while watching from an armchair.
By 15, he is the head of a bank which makes dirty money clean.
He can manipulate people to his means.
Currently the only person who can match Johan is Lelouch, but considering his egocentricity, Johan wins.
E.g. Although Light Yagami is the protagonist, you can consider from his homicidal acts that he is a villain.
My favorite villain is Johan Liebert from Monster:
Reasons:
He has an IQ of at least 150.
He is a sociopath and caused 50 people to kill each other while watching from an armchair.
By 15, he is the head of a bank which makes dirty money clean.
He can manipulate people to his means.
Currently the only person who can match Johan is Lelouch, but considering his egocentricity, Johan wins.