Pain, Madara and Orochimaru are the main badguys.
Pain is a propecised god of all ninja who can't be beaten and wants to create a Hiroshima no Jutsu to end all war. Madara is a crazy bastard who has pretty much masterminded all the tragedy in the two main character's backstories. Orochimaru, while not as powerful as the other two, is a rogue ninja from the Leaf who wants to obtain immortality and learn every jutsu that exists. He's also the most persistent villain in the series, he shows up all the damn time.