The full list is here, please enjoy. Thanks to AAAutin for helping greatly with the tallying process, smirnoff for finding and hosting the cover images, and everybody who submitted a ballot. See you in two years!
Full tally spreadsheet.1. Middle-Earth Books - J.R.R. Tolkien
2. 1984 - George Orwell
3. The Complete Works of William Shakespeare - William Shakespeare
4. Harry Potter - J.K. Rowling
5. Dashiell Hammett: Complete Novels - Dashiell Hammett
6. Slaughterhouse-Five - Kurt Vonnegut
7. Crime and Punishment - Fyodor Dostoevsky
8. The Catcher in the Rye - J.D. Salinger
9. The Ender's Game Series - Orson Scott Card
10. The Road - Cormac McCarthy
11. Fahrenheit 451 - Ray Bradbury
12. Calvin and Hobbes - Bill Watterson
13. Complete Works of Charles Dickens - Charles Dickens
14. In Cold Blood - Truman Capote
15. "L.A. Quartet" - James Ellroy
16. The Hitchhiker's Guide to the Galaxy Series - Douglas Adams
17. Starship Troopers - Robert A. Heinlein
18. The Great Gatsby - F. Scott Fitzgerald
19. A Song of Ice and Fire - George R.R. Martin
20. The Bible
21. The Robot Series - Isaac Asimov
22. To Kill a Mockingbird - Harper Lee
23. Watchmen - Alan Moore and David Gibbons
24. A Confederacy of Dunces - John Kenedy Toole
25. Blood Meridian, or the Evening Redness in the West - Cormac McCarthy
26. Catch-22 - Joseph Heller
27. The Foundation series - Isaac Asimov
28. The Hannibal Lecter Series - Thomas Harris
29. Watership Down - Richard Adams
30. Complete Works of Oscar Wilde - Oscar Wilde
31. The Dune Series - Frank Herbert
32. The Underworld USA Trilogy - James Ellroy
33. His Dark Materials Trilogy - Philip Pullman
34. Pride and Prejudice - Jane Austen
35. Animal Farm - George Orwell
36. Brave New World - Aldous Huxley
37. Cloud Atlas - David Mitchell
38. Fight Club - Chuck Palahniuk
39. The Complete C.S. Lewis Signature Classics - C.S. Lewis
40. The Short Novels of John Steinbeck - John Steinbeck
41. The Trial - Franz Kafka
42. American Psycho - Bret Easton Ellis
43. Lolita - Vladimir Nabokov
44. The Count of Monte Cristo - Alexandre Dumas
45. The Curious Incident of the Dog in the Night-Time - Mark Haddon
46. The Giver - Lois Lowry
47. A People's History of the United States - Howard Zinn
48. Alice in Wonderland - Lewis Carroll
49. Bone - Jeff Smith
50. The Complete Sherlock Holmes - Arthur Conan Doyle
51. The Dark Tower - Stephen King
52. The Stand - Stephen King
53. The Stranger - Albert Camus
54. Trainspotting - Irvine Welsh
55. A Clockwork Orange - Anthony Burgess
56. As I Lay Dying - William Faulkner
57. Cosmicomics - Italo Calvino
58. Howl and Other Poems - Allen Ginsberg
59. Jane Eyre - Charlotte Brontë
60. Never Let me Go - Kazuo Ishiguro
61. Oxford Time Travel - Connie Willis
62. Portnoy's Complaint - Philip Roth
63. The Godfather - Mario Puzo
64. All Quiet on the Western Front - Erich Maria Remarque
65. Dr. Jekyll and Mr. Hyde - Robert Louis Stevenson
66. "Flannery O'Connor : Collected Works" - Flannery O'Connor
67. Guns, Germs, and Steel: The Fates of Human Societies - Jared Diamond
68. If on a winter's night a traveler - Italo Calvino
69. Jennifer Government - Max Barry
70. Norwegian Wood - Haruki Murakami
71. The Complete Tales and Poems of Winnie-the-Pooh - A.A. Milne
72. The Forever War - Joe Haldeman
73. The Things They Carried - Tim O'Brien
74. At Swim, Two Boys - Jamie O'Neill
75. East of Eden - John Steinbeck
76. Glitz - Elmore Leonard
77. I, Lucifer - Glen Duncan
78. Midnight's Children - Salman Rushdie
79. Moonraker's Bride - Madeleine Brent
80. On the Road - Jack Kerouac
81. Perfume - Patrick Süskind
82. Stranger in a Strange Land - Robert A. Heinlein
83. The Chronicles of Narnia - C.S. Lewis
84. The Martian Chronicles - Ray Bradbury
85. The Shining - Stephen King
86. The Time Quintet - Madeleine L'Engle
87. Twinkle, Twinkle, "Killer" Kane (The Ninth Configuration) - William Peter Blatty
88. Farnham's Freehold - Robert A. Heinlein
89. The Phantom Tollbooth - Norton Juster