Let's look at all the villains in Naruto.
>Zabuza / Haku
>Gato
>Orochimaru / Kabuto
>Dosu / Kin / Zaku
>Chuunin exams Gaara
>Deidara
>Sasori
>Hidan
>Kakuzu
>Pain / Konan
>MS Sasuke
>Tobi / Obito
>Kisame
>Pre Itachi
>Madara
I choose Orochimaru. Unlike many villains who only value and wish for peace (Obito, Nagato, Madara), Orochimaru only wanted to discover the many ninjutsu's and secrets of the ninja world. He also wanted to be immortal. Conducting many experiments on his prisoners and unlocking and finding forbidden jutsu. He started to act like this supposedly when his parents died (which is better outcome than a girl you liked dying) .
The only ones who would even come close to Orochimaru are Kisame, Deidara, Kakuzu and Hidan as they had no goody goody image for their actions. They just did what they did because they were either ordered or they witnessed a bad experience like with Sasori losing his parents (same with Orochimaru) he in returned became a great puppet master and in return became rogue and killed the previous kazekage. Kisame killed his pass comrades and abandoned the mist village and joined the Akatsuki. He ate his own life just to not let the leaf ninja get the intel. Kisame only cared for accomplishing what was right for his mission. Emotions and comfort are not even valuable to Kisame as he truly thinks and acts like a shark. Hidan and Kakuzu are just mindless immortal fiends who kill for the fun of it. They are arguable the best villains but they have no drive and just do it for no reason which kind of defeats the purpose of being a villain. Most villains turn into villains for a certain reason and these two immortal beings don't really have a reason other than to be immortal and please their god (Jashin). Deidara only cares for his art and was even known for being a bomb terrorist.
Orochimaru is the best villain because he always has another plan if the first one fails and most of his plans end in despair and destruction like with the Leaf destruction and the killing of the third Hokage. His infamous label of killing many innocent people and even creating his own imposing village. This guy is the epitome of a good villain and people even fear this guy from just the sound of his name. Kakashi shit his pants from just the presence of this guy back in part 1.
Orochimaru makes the other villains look like baby cakes, before he changed his attitude when he was brought back and decided to be a father figure for Sasuke. Most characters are ruined through Edo Tensei and that's why Orochimaru will always be the best villain before he died.
