Madara and Orochimaru are pretty much the only legitimate villains in this series/manga. Rest either have some tragic background story with their butthurt being their motivation or are relative fodder.
BOSS of ALL Villians:- Madara Uchiha, hands down please.
* Orochimaru:- I might have put him into the boss title, he is so badass, powerful, indestructible, and really what called EVIL.
* Sasori:- Badass look, insanely powerful, right attitute for villian.
* Nagato:- Quite Badass, godly, powerful, mysterious, also nearly deserve boss title.
Obito: Because even tho he has gone the wrong way, i just want him to see the light again.
Madara: Because considering how baddass, powerful, and infamous he is, he seems to have the mentality of a kid.
Orochi: The man just does not die. That in itself is pretty baddass. would like to see him take on Dragon Sage Mode.