1. Thanos
2. Loki
3. Killmonger
4. Winter Soldier
5. Namor
6. Scarlet Witch
7. Kang
8. Vulture
9. Ultron
10. Mysterio
11. Zemo
12. High Evolutionary
13. Galactus
14. Cassandra Nova
15. Green Goblin
16. Kingpin
17. Xu Wenwu
18. Ronan
19. Ego
20. Hela
21. He Who Remains
22. The Leader
23. Dar-Benn
24. Agatha Harkness
25. Gorr
26. Red Skull
27. Death
28. Verussa
29. Arthur Harrow
30. Kaecilius
31. Ikaris
32. The Hood
33. Taskmaster
34. Ghost
35. Iron Monger
36. Aldrich Killian
37. Void
38. Gravik
39. Karli Morgenthau
40. Yellow Jacket
41. Whiplash
42. Abomination
43. Yon-Rogg
44. Kamran
45. Malekith

Some ranked here are based on contributions in multiple projects, such as Loki in The Avengers, as well as, his first appearance in Thor.

I made the decision to only choose one villain per film or show. If there was ever a question of who it would be, I generally chose the primary antagonist of the hero in the third-act.