This kind of depends on how you define villain. If you mean the guy that everyone hates, it's easy. If you mean the one who is evil and does the best job at it, then it's a little more difficult.
Shou Tucker - Full Metal Alchemist
If you choose the person that is universally hated as best villain, this guy is the hands down winner. I can't think of anyone that's a fan of his.
Souske Aizen - Bleach Aizen, former Captain of Squad 5, leader of all Arrancars. Nearly as powerful as Head Captain Yamamoto even during his time in Soul Society, and after his subjagation of the Hogyoku, he literally becomes immortal. Able to take on nearly every Captain, Vizard, and Vice-Captain single handedly. A man who mastered every form of Shinigami combat, is able to plan out war 100 years in advance, and able to deceive nearly everybody in the entire series. Someone who's power is so beyond normal, that he eventually decides to try and destroy the Soul King (God, basically) by himself. Aizen is the perfect villain... He stands back and let's others do his dirty work for him and not because he's a coward but he because he believes he has no equal... Unlike most villains that just wanna destroy everything is a game to Aizen.. Like a giant game of chess he allows things to play out because he believes he will come on top every time.. Aizen is the true King of Villains