I'm not sure if it has been mentioned, But I'd consider the Millennium Earl from D.Gray-man to a competent villain. He has an eccentric and friendly outer appearance a majority of the time, but that's to hide his true self. His main goal is to destroy God and bring the world to the brink of death.
By putting on his 'kindly grandfather-like' facade, he manages to convince people to bring the souls of their loved ones back to life and into an 'Akuma Skeleton'. He then controls the Akuma to kill the person and impersonate them and evolve to higher forms.
A greater step to this is that he has the Noah family -- superhuman descendants of Noah -- on his side as well, and each one of them are quite formidable.
In fact, 90% of Japan is dead/populated by Akuma.
Even though his goals are evil, he's still kind enough to buy a flower off of a girl selling them, and he treats the Noah family like a family of his own.




