Orochimaru no contest.. he actually had true evil intentions and was great at manipulation.. no villain so far has come close to him
Aizen Sousuke
Obito surpasses him in the manipulation abilities .
Obito may be stronger, but he's a bland character.
Orochimaru has charisma, the air of genius and disregard for ethicality. Yet, he's not above praising his opponents and gives credit where it's due, add that to his teasing attitude, and you have a great villain.