This was tough because, like Pixote said, defining "horror" is a difficult task. Some films, like Aliens, Shaun of the Dead, or Silence of the Lambs, can certainly be called horror films, but I had to cut them out, as much as I love them. That's not to say I didn't include other similar films (see Army of Darkness). So I guess my decisions were completely arbitrary and based on how I was feeling when making the list. I also decided to leave off a lot of the 50s giant monster/nuclear war films that I love so much, requisitioning them to the "sci-fi" genre (again, pretty arbitrary). All this nonsense leaves me with the following list.
100. Session 9 (Anderson, 2001)
99. The Devil's Backbone (Del Toro, 2001)
98. At Midnight I'll Take Your Soul (Marins, 1964)
97. Blood for Dracula (Morrissey, 1974)
96. Black Sunday (Bava, 1960)
95. High Tension (Aja, 2003)
94. Dracula (Browning, 1931)
93. The Abominable Dr. Phibes (Fuest, 1971)
92. Dust Devil (Stanley, 1992)
91. Mad Love (Freund, 1935)
90. The Cabinet of Dr. Caligari (Wiene, 1920)
89. The Hunger (Scott, 1983)
88. Theater of Blood (Hickox, 1973)
87. Repulsion (Polanski, 1965)
86. Sisters (De Palma, 1973)
85. The Descent (Marshall, 2005)
84. Quatermass and the Pit (Baker, 1967)
83. Santa Sangre (Jodorowsky, 1989)
82. Nosferatu (Murnau, 1922)
81. Henry: Portrait of a Serial Killer (McNaughton, 1986)
80. Horror of Dracula (Fisher, 1958)
79. Flesh for Frankenstein (Morrissey, 1973)
78. A Tale of Two Sisters (Kim, 2003)
77. Night of the Demon aka Curse of the Demon (Tourneur, 1957)
76. Trollhunter (Ovredal, 2010)
75. Bad Taste (Jackson, 1987)
74. Diabolique (Clouzot, 1955)
73. Jigoku (Nakagawa, 1960)
72. Little Otik (Svankmajer, 2000)
71. The Invisible Man (Whale, 1933)
70. The Blob (Russell, 1988)
69. The Beyond (Fulci, 1981)
68. Deep Red (Argento, 1975)
67. Martin (Romero, 1977)
66. Haxan: Witchcraft Through the Ages (Christensen, 1922)
65. Halloween III: Season of the Witch (Wallace, 1982)
64. Creepshow (Romero, 1982)
63. Eyes Without a Face (Franju, 1960)
62. Phantasm (Coscarelli, 1979)
61. Monster Squad (Dekker, 1987)
60. Pan's Labyrinth (Del Toro, 2006)
59. The Changeling (Medak, 1980)
58. Scanners (Cronenberg, 1981)
57. The Mist (Darabont, 2007)
56. Poltergeist (Hooper, 1982)
55. The Brood (Cronenberg, 1979)
54. From Beyond (Gordon, 1986)
53. Witchfinder General (Reeve, 1968)
52. Audition (Miike, 1999)
51. Creature From the Black Lagoon (Arnold, 1954)
50. Peeping Tom (Powell, 1960)
49. Nosferatu: Phantom Der Nacht (Herzog, 1979)
48. Carnival of Souls (Harvey, 1962)
47. The Masque of Red Death (Corman, 1964)
46. The Wolf Man (Waggoner, 1941)
45. Hellraiser (Barker, 1987)
44. Cabin in the Woods (Goddard, 2012)
43. Onibaba (Shindo, 1964)
42. [REC] (Balaguero & Plaza, 2007)
41. Jacob's Ladder (Lyne, 1990)
40. Night of the Creeps (Dekker, 1986)
39. Don't Look Now (Roeg, 1973)
38. Kwaidan (Kobayashi, 1964)
37. Eraserhead (Lynch, 1977)
36. The Fog (Carpenter, 1980)
35. The Devil Rides Out (Fisher, 1968)
34. An American Werewolf in London (Landis, 1981)
33. Dead Ringers (Cronenberg, 1988)
32. Hausu (Obayashi, 1977)
31. Trick 'r Treat (Dougherty, 2007)
30. The Wicker Man (Hardy, 1973)
29. Cemetery Man (Soavi, 1994)
28. Zombi II (Fulci, 1979)
27. Freaks (Browning, 1932)
26. Frankenstein (Whale, 1931)
25. 28 Days Later (Boyle, 2002)
24. Let the Right One In (Alfredson, 2008)
23. The Haunting (Wise, 1963)
22. Day of the Dead (Romero, 1985)
21. Rosemary's Baby (Polanski, 1968)
20. Re-Animator (Gordon, 1985)
19. Suspiria (Argento, 1977)
18. Dead Alive (Jackson, 1992)
17. Evil Dead II (Raimi. 1987)
16. Return of the Living Dead (O'Bannon, 1985)
15. Halloween (Carpenter, 1978)
14. Army of Darkness (Raimi, 1993)
13. Bride of Frankenstein (Whale, 1935)
12. Invasion of the Body Snatchers (Kaufman, 1978)
11. The Texas Chainsaw Massacre (Hooper, 1974)
10. Jaws (Spielberg, 1975)
9. The Shining (Kubrick, 1980)
8. Videodrome (Cronenberg, 1983)
7. Psycho (Hitchcock, 1960)
6. The Fly (Cronenberg, 1986)
5. Alien (Scott, 1979)
4. The Thing (Carpenter, 1982)
3. Dawn of the Dead (Romero, 1978)
2. Night of the Living Dead (Romero, 1968)
1. The Evil Dead (Raimi, 1981)