Hmm well there are many types of villains out there! For me these villains tops my list -
Orochimaru: Most meancing and plain ass creepy. His intentions were evil and selfish because his intention wasn't to conquer the whole world but actually to be immortal.
Nagato's Six Paths of Pain: Most destructive villain out there (before the 4th War) to cause havoc and destroy the Leaf in a single blow. Though his main true intention was to actually bring peace even if his methods were a bit evil. Redeemed himself by reviving back the Leaf's villagers and shinobis.
Danzou: A proud man who loves his country, takes a serious cold approach in order to protect his village by any means necessary. Hence why he created ANBU Root. During his final moments he did one last thing for his country by crushing shisui's eyes (Who knows what Tobi could have done with that)
Kabuto: A simple looking yet blackmailing villain. Power hungry in an attempt to gain powers of the SO6P.
Tobi: A very manipulative and deceptive villain by using others as puppets and pulling the strings from the background. After world peace like Nagato...or is he?
Madara: Plain arrogant villain who just wants to see the world suffer.
Cant really say much for Kabuto,Tobi and Madara because we dont know their true intentions yet.