So, nowhere really says who the main villains of each season is but having seen Seasons 1-6 and read a bit about 7, I pretty much figured it out.
If you haven't seen it, most of these will be spoilers.
Season 1 - Jamie Moriarty (obviously)
Season 2 - Guillaume De Soto, seeing as how the main reason Mycroft is in New York is to take him down. Tim Sherrington only took over for the last two episodes, where Le Milieu still had a presence. (I'm not sure if De Soto was returned to power after Mycroft was exposed to Le Milieu and faked his death but it sounds like he may have been killed by Sicilian mafia in Season 6?) One might count Sherrington anyway as final antagonist of the season.
Season 3 - Del Gruner, as the nemesis to Kitty, the guest star for the first half of the season. Oscar Rankin only had an impact on two episodes even if the second was the finale and he caused Sherlock's relapse, but one could count him.
Season 4 - Joshua Vikner, obviously, as the new leader of Moriarty's organization who wants Morland, guest star of the season, dead. He must've been based off the Robert Downey Jr. films' Moriarty.
Season 5 - Tyus Wilcox, the supreme leader of the gang SBK who has a presence throughout the season and with Shinwell, the guest star of the season, as the informant trying to take them down.
Season 6 - Michael Rowan, who happens to be the guest star of the season rather than the nemesis of the guest star of the season. This serial killer has more of a presence in the season than Moriarty.
Season 7 - From what I can tell, Odin Reichenbach.