Supernatural has its own page for who the main villain of each season is. I don't know if this wiki's going to get one but basically I'll make a list and see if we can agree on it.
Also listing secondary antagonists, but forgive me if I don't remember a whole lot from Seasons 3 onward
Main - Victor Drazen. At first it was Gaines, but he was working for Andre, and it's later revealed Victor was somehow in contact with Andre the whole time he was in prison and thus he seems to be the mastermind behind the day's events. Ultimately the highest up the chain of command here.
Secondary - Andre Drazen, Ira Gaines. Also Kevin Carroll, Alexis Drazen, Jovan Myovic, Jonathan Matijevich, Dan Mounts, Jamey Farrell, and Nina Myers. And Carl Webb and Sherry Palmer for David Palmer's subplot.
Main - Peter Kingsley, who orchestrated the whole events. Syed Ali planted the bomb for his own reasons, but he wasn't in on Kingsley's plan to start a war, and Kingsley gave him the bomb, which was a big part of his plan which continued past the detonation of the bomb.
Bigger Bad - Max, who was the mastermind of the plan, but only appeared in two episodes. And, later, the game, where Jack finally kills him.
Main - Stephen Saunders. At least for the second half; I don't recall Ramon Salazar being directly involved with him or a pawn in his plan, just seeking the virus for his own reasons, so perhaps he'd count as the main villain of the first half, splitting the season in two like Once Upon A Time, also on a similar scale to the systems of Seasons 6, 8, and Live Another Day (though while Ramon's run was exactly half the season, Fayed, Samir, and Margot lasted longer). Although, Saunders seemed the bigger threat because he got the virus, where Ramon was seeking it to sell to terrorists for a profit.
Main - Habib Marwan, easily. He's the leader of the terrorist cell which is the main threat of the whole season.
Main - Charles Logan for the conspiracy, Vladimir Bierko for the terrorists. The bigger focus seemed to be on the conspiracy, to which Bierko was a pawn, but Bierko was a bigger threat to Los Angeles.
Bigger Bad - Graem Bauer, who plays a similar role to Max, with Logan as Kingsley. By extension, Phillip Bauer, even though he didn't appear. And, according to Season 7, Alan Wilson, though he was quite clearly invented for Season 7 as a means of turning Tony evil on account of Graem and Phillip being dead, so his connection to them, and who had more power within their conspiracy, is never specified, since both Graem and Wilson are stated to have masterminded the plan.
Main - Abu Fayed for over half the season, as the leader of the terrorists and one of the most successful mass murderers in the show. Following his death, Phillip Bauer, with his plans to start a war, though he hardly does anything except kidnap his grandson.
Past here is where I Discontinuity the seasons, but to be fair I'll include them:
Main - Alan Wilson, the mastermind of the day's events. And, in one of the biggest stretches of the show, Season 5's events as well. Though some might consider him Max to Jonas Hodges's Peter Kingsley, and thus count Hodges. Also Benjamin Juma has been counted as well, can't remember how involved he was with Hodges and Wilson, he could be the Ramon Salazar/Abu Fayed.
Main - Samir Mehran for over half, then Charles Logan and Yuri Suvarov (who are inexplicably back from the dead and turned to the dark side, respectively) replace him shortly before he is killed to cover up Suvarov's involvement in Samir's plans.
Live Another Day:
I never actually saw this season, but...
Secondary - From the sound of things, Ian Al-Harazi