The ones I've read are in bold, even if I've only read some of a series I've marked it bold, Xanth has about a million books and I stopped reading them 20 years ago.
1. The Lord Of The Rings Trilogy, by J.R.R. Tolkien Read this over 20 times in middle school.
2. The Hitchhiker’s Guide To The Galaxy, by Douglas Adams Again, read this so many times I haven't read it in years. I also think I might like Long Dark Teatime of the Soul better, but that could be the familiarity equals contempt issue.
3. Ender’s Game, by Orson Scott Card I read this so late that by the time I got to it most of the concepts didn't seem new, from all the other authors "borrowing" them.
4. The Dune Chronicles, by Frank Herbert Loved it at the time, needs to be read in big chunks though, so reading this in middle school was what I remember the most.
5. A Song Of Ice And Fire Series, by George R. R. Martin It's on my list.
6. 1984, by George Orwell For school, good book though.
7. Fahrenheit 451, by Ray Bradbury Read this when my mom and dad were visiting friends, I used to borrow books from them and read while they hung out. Censorship bad mmkay?
8. The Foundation Trilogy, by Isaac Asimov Again read this one in middle school, just read them again a couple years ago.
9. Brave New World, by Aldous Huxley This was the book assigned to half my class that didn't get 1984, I read both.
10. American Gods, by Neil Gaiman On my list.
11. The Princess Bride, by William Goldman Love the movie, is the book as good?
12. The Wheel Of Time Series, by Robert Jordan Oh my god, I started reading these when I got out of basic training 20 years ago, I'm not reading any more until the last one is published. Great story, way too much stasis in the main characters. Power levels increase with the passing of time, but not maturity apparently.
13. Animal Farm, by George Orwell Again, for school, because some books are more equal than others.
14. Neuromancer, by William Gibson Considering how much I am into Cyberpunk, I've never read this.
15. Watchmen, by Alan Moore
16. I, Robot, by Isaac Asimov Classic Sci-Fi (Or is that Syfy now?)
17. Stranger In A Strange Land, by Robert Heinlein I read this, never really understood the big deal.
18. The Kingkiller Chronicles, by Patrick Rothfuss
19. Slaughterhouse-Five, by Kurt Vonnegut KVJ was an odd duck, but at least he wasn't drawing assholes in this one.
20. Frankenstein, by Mary Shelley Read this back in the mists of time.
21. Do Androids Dream Of Electric Sheep?, by Philip K. Dick This was actually in one of my literature books in High School, the class didn't read it, but I did when I was bored in class.
22. The Handmaid’s Tale, by Margaret Atwood
23. The Dark Tower Series, by Stephen King
24. 2001: A Space Odyssey, by Arthur C. Clarke Duh.
25. The Stand, by Stephen King I've read this, It, and the Bachman books, not a huge fan of Stephen but he writes books that are fun to read.
26. Snow Crash, by Neal Stephenson
27. The Martian Chronicles, by Ray Bradbury This used to confuse me so much when I was a kid.
28. Cat’s Cradle, by Kurt Vonnegut Can't remember which one this is but I read all his books.
29. The Sandman Series, by Neil Gaiman
30. A Clockwork Orange, by Anthony Burgess Hmm, anyone looked around lately?
31. Starship Troopers, by Robert Heinlein The movie made me angry with the heat of a million suns.
32. Watership Down, by Richard Adams Seen the movie, need to read the book.
33. Dragonflight, by Anne McCaffrey Back before everything on the planet could talk, and before she was sure this was a science fiction story.
34. The Moon Is A Harsh Mistress, by Robert Heinlein I love this book.
35. A Canticle For Leibowitz, by Walter M. Miller This dude writes two books, this one and a miserable sequel 30 years later and one of them hits the top 100 list? This one can make you think.
36. The Time Machine, by H.G. Wells I know I've read it, just can't remember when.
37. 20,000 Leagues Under The Sea, by Jules Verne
38. Flowers For Algernon, by Daniel Keys Sad story.
39. The War Of The Worlds, by H.G. Wells
40. The Chronicles Of Amber, by Roger Zelazny I have bought these books three times.
41. The Belgariad, by David Eddings
42. The Mists Of Avalon, by Marion Zimmer Bradley
43. The Mistborn Series, by Brandon Sanderson
44. Ringworld, by Larry Niven Just read these recently. Pretty good, something just hit me wrong.
45. The Left Hand Of Darkness, by Ursula K. LeGuin
46. The Silmarillion, by J.R.R. Tolkien Took a lot of effort to read through this one, not sure if it was worth it still.
47. The Once And Future King, by T.H. White
48. Neverwhere, by Neil Gaiman
49. Childhood’s End, by Arthur C. Clarke
50. Contact, by Carl Sagan Great book, ends abruptly.
51. The Hyperion Cantos, by Dan Simmons
52. Stardust, by Neil Gaiman
53. Cryptonomicon, by Neal Stephenson
54. World War Z, by Max Brooks
55. The Last Unicorn, by Peter S. Beagle I love this story.
56. The Forever War, by Joe Haldeman Great story and great premise.
57. Small Gods, by Terry Pratchett Terry is one of my favorites.
58. The Chronicles Of Thomas Covenant, The Unbeliever, by Stephen R. Donaldson Read this one a bit young. I just love to hate Thomas.
59. The Vorkosigan Saga, by Lois McMaster Bujold Picked this one up last year. Read them all way too quickly.
60. Going Postal, by Terry Pratchett Again, Sir Pratchett is the bomb.
61. The Mote In God’s Eye, by Larry Niven & Jerry Pournelle Larry Niven does collaborations really well. I wish there was no sequel.
62. The Sword Of Truth, by Terry Goodkind First five or six books are good, then it gets old constantly going from frying pan to fire.
63. The Road, by Cormac McCarthy
64. Jonathan Strange & Mr Norrell, by Susanna Clarke
65. I Am Legend, by Richard Matheson
66. The Riftwar Saga, by Raymond E. Feist
67. The Shannara Trilogy, by Terry Brooks I have been trying to collect the rest of the series without bankrupting myself.
68. The Conan The Barbarian Series, by R.E. Howard Read these on my phone via project Guttenheim.
69. The Farseer Trilogy, by Robin Hobb
70. The Time Traveler’s Wife, by Audrey Niffenegger
71. The Way Of Kings, by Brandon Sanderson
72. A Journey To The Center Of The Earth, by Jules Verne
73. The Legend Of Drizzt Series, by R.A. Salvatore
74. Old Man’s War, by John Scalzi Reading this one right now actually.
75. The Diamond Age, by Neil Stephenson
76. Rendezvous With Rama, by Arthur C. Clarke Waited 20 years or so for a sequel, then wished it hadn't been written.
77. The Kushiel’s Legacy Series, by Jacqueline Carey
78. The Dispossessed, by Ursula K. LeGuin
79. Something Wicked This Way Comes, by Ray Bradbury
80. Wicked, by Gregory Maguire
81. The Malazan Book Of The Fallen Series, by Steven Erikson
82. The Eyre Affair, by Jasper Fforde
83. The Culture Series, by Iain M. Banks
84. The Crystal Cave, by Mary Stewart
85. Anathem, by Neal Stephenson
86. The Codex Alera Series, by Jim Butcher Nice new flavor on magic and such.
87. The Book Of The New Sun, by Gene Wolfe Class A brain melt. I've read them several times and I just don't quite understand the whole thing still.
88. The Thrawn Trilogy, by Timothy Zahn
89. The Outlander Series, by Diana Gabaldan
90. The Elric Saga, by Michael Moorcock I was Elric for Halloween in 6th grade, nuff said.
91. The Illustrated Man, by Ray Bradbury Short stories wrapped up in a novel, Ray was weird.
92. Sunshine, by Robin McKinley
93. A Fire Upon The Deep, by Vernor Vinge
94. The Caves Of Steel, by Isaac Asimov
95. The Mars Trilogy, by Kim Stanley Robinson Only read the first one, meh.
96. Lucifer’s Hammer, by Larry Niven & Jerry Pournelle Loved it.
97. Doomsday Book, by Connie Willis
98. Perdido Street Station, by China Mieville
99. The Xanth Series, by Piers Anthony Peirs Anthony is really odd, fun writing but I'm not sure I could stand to read all 9 million books.
100. The Space Trilogy, by C.S. Lewis Great good vs. Evil books.
I plan on reading more Gaimon, I really liked Good Omens. LeGuin has been on my read list for ages, half price books doesn't love her and it's hard to figure out where to start.
I'm surprised at a couple authors that didn't make it. Harry Harrison, CJ Cherryh, L Sprague de Camp, a couple others I can't think of. I Have No Mouth and I Must Scream should have made it. Ellison is such a jackass though.
Obviously you are dealing with the issue of comparing new books to old books. Is Jim Butcher a better writer than Gene Wolfe? I don't think so, but at this time his books are out there on the end caps. Seems like just as much name recognition as anything else was a factor on these.