Supernatural Wiki has a page entitled "Big Bad", which is a term for main villains originating from Buffy the Vampire Slayer.
The Masterminds page also has the masterminds of smaller plans that were more of a subplot to the season, like Roger Stanton, Bruce Carson, or Joe Wald who worked for Syed Ali. And Ali himself, who planted the bomb for his own reasons, but was a pawn for Max and Kingsley as part of their bigger scheme to start a war. Though not strictly main villains of the season, they definitely belong in that category.
Ramon Salazar is in that category too, as is Hector. I'll finish Season 3 before deciding whether he's as much the main villain of Season 3 as Saunders. Again, they are seeking the virus completely for their own reasons for the first half, Saunders doesn't get involved until the second half.