Tobi (tried to keep it as spoiler free as possible for anyone who's way behind, like me!)
Tobi's identity is a bit of a mystery for a while. It was spoiled for me that he's not who I'm supposed to think he is at this point, and then I accidentally stumbled upon hints leading me to his actual identity, but for simplicity, I'll just stick with Tobi! Tobi plays himself off as ditsy , comic-relief Akatsuki noob, but is actually a manipulative mastermind. I still have much to learn about him, and I have a feeling some of that will make me question his status as a villain, as seems to happen a lot with Naruto, but as far as I've gotten, I think he would be my favorite villain.
This was a challenge for me because, as I said, the line defining villains gets pretty blurry, especially with this anime! ^I think Armin puts it best! I had a small handful of close competitors for my favorite villain, so here are some of the other top contenders:
The classic, Orochimaru is an interesting character, to say the least. One of the Legendary Sannin of Konoha, he had a maddening curiosity, which led him to conduct research on countless victims, viewed only as pawns so that he could master all jutsu and surpass his sensei, the Third Hokage. This white snake sustained his life by transferring himself to new bodies, achieving a sort of immortality. His downfall was his desire to claim Sasuke Uchiha as his next vessel in order to acquire the Sharingan. Again, I get the sense that there is more for me to learn about this character.
Orochimaru's right hand man, Kabuto is a bit of an enigma. Specializing in intelligence gathering, Kabuto spends much of his time acting as a spy for various parties, so it is challenging to pin-point exactly who's side he's on or what his end-goal is. I look forward to seeing how his schemes unfold.
Pain - note, I'm not talking about Nagato, but specifically his Pain persona - was the leader of the Akatsuki. His goal was to use pain as a lesson to achieve peace, so he is one of those cases that is easy to debate whether or not he should actually be considered a villain.