1) Thanos - In the background of the all the MCU to Date and the main character in Avengers: Infinity War.
2) Loki - Thor's Brother the God of Mischief was the main villain of the first Avengers Movie. Has become unclear if he is a villain anymore sometimes helps the good guys when it is convenient and helps him in some way.
3) Kilgrave (The Purple Man) - Played by David Tennant in Netflix series Jessica Jones.
4) Vulture - Played by the awesome Michael Keaton in
Spider-Man:Homecoming
5) Kingpin - Appears in Netflix Daredevil series.
6) Ego - Played by Kurt Russell in Guardians 2
7) The Winter Soldier - Again some will say not a villain but if you just watch Captain America: The Winter Soldier he is a the brainwashed villain of that movie.
8) Baron Zemo - does not fight any of the Avengers but sets them against each other, I am hoping this character comes back in future movies. Appears in Captain America: Civil War
9) Eric Killmonger - I know a lot of people will have him much higher on their lists. Appears in Black Panther.
10) Kaecillius - Appears in Doctor Strange.
I know people will disagree with my list that is fine just a bit of fun. Hela and Ultron nearly made my list ;)