Board Thread:TV Show Discussion/@comment-1031724-20160522234612

What makes Game of Thrones unique is that it doesn't strictly have a "main villain", at least not in the sense of Palpatine, Sauron, Voldemort, Loki, Frieza, Queen Beryl, The Master, Lucifer, etc.

There being many villains, and many storylines, I would then classify the most prominent villain in each story of each season a main villain. So, here's my list:

Daenerys doesn't seem to have any long lasting enemies in Seasons 3 and 4, as she defeats them too quickly and is more focused on being queen of Meereen and keeping the freedom and peace there. 
 * Cersei Lannister - King's Landing story, Season 1
 * Jaime Lannister - King's Landing story, Season 1
 * Viserys Targaryen - Daenerys's story, Season 1
 * Joffrey Baratheon - King's Landing story and Robb's story, Seasons 2 and 3
 * Tywin Lannister - Aria's story, Season 2; King's Landing story, Season 4
 * Theon Greyjoy - Winterfell story (and, in a sense, Robb's story), Season 2
 * Balon Greyjoy - Winterfell story, Season 2 (guy behind the guy, as he convinces Theon to turn on Robb)
 * Mance Rayder - Jon's story, Seasons 2-4
 * Pyat Pree - Daenerys's story, Season 2
 * Ramsay Bolton - Theon's story, Season 3; Winterfell story, Seasons 5 and 6
 * The High Sparrow - King's Landing story, Seasons 5 and 6
 * Roose Bolton - Winterfell story, Season 5
 * Ellaria Sand - Dorn story, Seasons 5 and 6
 * The Night's King - Jon's story, Seasons 5 and 6
 * Sons of the Harpy - Daenerys's story, Seasons 5 and 6
 * Slave masters - Daenerys's story, Seasons 5 and 6 (it's revealed they're behind the Sons of the Harpy)