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. Jean Grey
22. He Who Remains
23. The Leader
24. Dar-Benn
25. Agatha Harkness
26. Gorr
27. Red Skull
28. Death
29. Verussa
30. Arthur Harrow
31. Kaecilius
32. Ikaris
33. The Hood
34. Taskmaster
35. Ghost
36. Iron Monger
37. Aldrich Killian
38. Void
39. Gravik
40. Karli Morgenthau
41. Yellow Jacket
42. Whiplash
43. Abomination
44. Yon-Rogg
45. Kamran
46. 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.