Pyramid Head is listed twice. In his place can suggest, hm... Vaati, from Zelda?
Edit: For convenience, sorted things by series -
1. Bowser (Mario series)
14. Wario (Mario series)
40. Smithy (Super Mario RPG)
43. Dimentio (Super Paper Mario)
55. Waluigi (Mario)
22. Donkey Kong (Donkey Kong arcade game)
2. Ganondorf (LoZ series)
3. GlaDos (Portal)
4. The Gravemind(Halo)
5. Giovanni(Pokemon)
54. Team Galactic (Pokemon)
6. The Agency(Crackdown)
7. Kefka Palazzo (Final Fantasy Series)
8. Prince Luca Blight (Suikoden Series)
9. Sigma (Mega Man X Series)
42. Dr.Wily (Megaman series)
48. Lord Weil (Megaman Zero)
10. Geese Howard (Fatal Fury)
11. Dahlia Hawthorne (Phoenix Wright 3)
44. Kristoph Gavin (Ace Attorney: Apollo Justice)
12. Nobunaga Oda (aka "Devil King") (Sengoku BASARA (aka "Devil Kings") version)
13. Deviculus (Brutal Legend)
15. King K. Rool (DK series)
17. M. Bison (Street Fighter)
18 / 61. Pyramid Head (Silent Hill)
19. Goro (Mortal Kombat)
20. Diablo (Diablo)
21. Pinky, Inky, Blinky, Clyde, and Sue [The Ghosts] (Pac Man series)
23. Darth Vader (Star Wars)
24. Carlito Keyes (Dead Rising)
25. Samurai Goroh (F-Zero series)
26. Cervantes (Soul Calibur series)
27. Dr Robotnik/Eggman (Sonic series)
28. Heihachi Mishima (Tekken)
29. Ashtar (Ninja Gaiden 2 NES)
30. Game Master Arino (Retro Game Challenge)
31. Andrew Ryan(Bioshock)
32. President Eden(Fallout 3)
33. The Special Infected(Left 4 Dead)
34. The Lich King (Warcraft series)
35. Eyedol (Killer Instinct)
16. Revolver Ocelot (Metal Gear Solid)
36. Liquid Snake (Metal Gear Solid)
37. Solidius Snake (Metal Gear Solid)
59. Psycho Mantis (Metal Gear Solid)
38. Albert Wesker (Resident Evil)
39. Master Hand (Super Smash Bros)
41. Overlord Zenom(Disgaea 2)
42. Gruntilda(Banjo Kazooie)
45. Lavos (Chrono Trigger)
46. Bad Girl (No More Heroes)
47. Master Van (Tales of the Abyss)
49. Dhoulmagus (Dragon Quest VIII)
50. Zoda (StarTropics)
51. Super Drunk (Bubble Bobble)
52. Smash Daisaku (aka Colonel Red) (Gunstar Heroes)
53. Zur Pa Iyah (Guardian Heroes)
56. Frank Fontaine (Bioshock)
57. SHODAN (System Shock)
58. Ridley (Metroid)
60. Scissorman (Clock Tower series)
62. Sarah Kerrigan (StarCraft)
63. Giygas (Mother Series)
64. Grandmaster Meiou (Strider Hiryu)