... except, of course, it's not. They've chosen one novel per author. In reality, it would be bizarre to expect that the very best novelists wrote only one of the top 100 novels. (Also, their choices sometimes seem to me to be questionable).
I also question the usefulness of selecting novels from, oh, the last 50 years: we're too close. Too much of our reaction may be to shared memes which don't affect our reaction to novels from 200 years ago. (As the novels are arranged roughly chronologically, this translates as "anything after Catch-22" (which was published in 1961). I'm also dubious about about a quarter of the list falling into this recent category on more general grounds: there's a distortion of perspective distinct from our assessment of quality which tends to make recent names more familiar. (You'll note that I haven't read many of the recent selections, as my tastes diverge from "mainstream" literature in the period, and the major authors I have read, like Pynchon, don't seem to get a look in.)
I've bolded all the books I own, italicized all those I've read but don't own, and added comments as seemed appropriate.
1. Don Quixote, Miguel De Cervantes[A parody of the prose romance; not a novel. If you include Cervantes you need to include Amadis and Arcadia as well.]
2. Pilgrim's Progress, John Bunyan [Not a novel but a religious allegory]
3. Robinson Crusoe, Daniel Defoe [A counterfeit autobiography. Not a novel.]
4. Gulliver's Travels, Jonathan Swift [Another counterfeit autobiography. Not a novel. Also probably not as great a piece of work as The Tale of A Tub.]
5. Tom Jones, Henry Fielding [The first actual novel on the list, by normal definitions. There are earlier novels as we use the term today -- the Tale of Genji is the obvious one -- but just being a long piece of prose fiction does not a novel make. Some later inclusions are also questionable, but they've at least been influenced to a degree by conventions springing from Fielding.]
6. Clarissa, Samuel Richardson [I've read Pamela, but not Clarissa.]
7. Tristram Shandy, Laurence Sterne
8. Dangerous Liaisons, Pierre Choderlos De Laclos
9. Emma, Jane Austen
10. Frankenstein, Mary Shelley
11. Nightmare Abbey, Thomas Love Peacock
12. The Black Sheep, Honore De Balzac [Um. Is this better than Le père Goriot?]
13. The Charterhouse of Parma, Stendhal
14. The Count of Monte Cristo, Alexandre Dumas [Maybe. If you let Buchan in, Dumas probably deserves a place as well. But wouldn't Zola's Germinal be a better choice?]
15. Sybil, Benjamin Disraeli
16. David Copperfield, Charles Dickens [Dickens is not really my favourite Victorian author, but he probably deserves several novels in the top 100]
17. Wuthering Heights, Emily Bronte
18. Jane Eyre, Charlotte Bronte
19. Vanity Fair, William Makepeace Thackeray
20. The Scarlet Letter, Nathaniel Hawthorne
21. Moby-Dick, Herman Melville [Arguably not a novel, given its structure and focus]
22. Madame Bovary, Gustave Flaubert {Defines the novel for the 20th century, basically.]
23. The Woman in White, Wilkie Collins [I'd definitely rank The Moonstone above this.]
24. Alice's Adventures In Wonderland, Lewis Carroll
25. Little Women, Louisa M. Alcott
26. The Way We Live Now, Anthony Trollope
27. Anna Karenina, Leo Tolstoy
28. Daniel Deronda, George Eliot [Probably should have several novels here, including Middlemarch and The Mill on the Floss]
29. The Brothers Karamazov, Fyodor Dostoevsky
30. The Portrait of a Lady, Henry James [James probably wrote at least 5 books that should be on this list. But is this better than The Ambassadors or The Wings of the Dove?]
31. Huckleberry Finn, Mark Twain
32. Dr Jekyll and Mr Hyde, Robert Louis Stevenson
33. Three Men in a Boat, Jerome K. Jerome
34. The Picture of Dorian Gray, Oscar Wilde
35. The Diary of a Nobody, George Grossmith
36. Jude the Obscure, Thomas Hardy [Again, better than Tess? Both should be on the list.]
37. The Riddle of the Sands, Erskine Childers[It's a great spy story, but should it be here and, say, not Ashenden?]
38. The Call of the Wild, Jack London
39. Nostromo, Joseph Conrad [Several of his novels should be on the list.]
40. The Wind in the Willows, Kenneth Grahame
41. In Search of Lost Time, Marcel Proust [Obviously deserves to be here, but it seems to be the only roman-fleuve. Surely Powell and Raven should get a look in?]
42. The Rainbow, D. H. Lawrence
43. The Good Soldier, Ford Madox Ford
44. The Thirty-Nine Steps, John Buchan [Come on, be serious. Not nearly the best novel by Buchan, and I'm not sure that any are up to the level required, much as I like Buchan.]
45. Ulysses, James Joyce
46. Mrs Dalloway, Virginia Woolf
47. A Passage to India, E. M. Forster
48. The Great Gatsby, F. Scott Fitzgerald
49. The Trial, Franz Kafka
50. Men Without Women, Ernest Hemingway
51. Journey to the End of the Night, Louis-Ferdinand Celine
52. As I Lay Dying, William Faulkner
53. Brave New World, Aldous Huxley
54. Scoop, Evelyn Waugh [Not Men At Arms?]
55. USA, John Dos Passos
56. The Big Sleep, Raymond Chandler
57. The Pursuit Of Love, Nancy Mitford
58. The Plague, Albert Camus
59. Nineteen Eighty-Four, George Orwell
60. Malone Dies, Samuel Beckett
61. Catcher in the Rye, J.D. Salinger
62. Wise Blood, Flannery O'Connor
63. Charlotte's Web, E. B. White
64. The Lord Of The Rings, J. R. R. Tolkien
65. Lucky Jim, Kingsley Amis
66. Lord of the Flies, William Golding
67. The Quiet American, Graham Greene
68 On the Road, Jack Kerouac
69. Lolita, Vladimir Nabokov
70. The Tin Drum, Gunter Grass
71. Things Fall Apart, Chinua Achebe
72. The Prime of Miss Jean Brodie, Muriel Spark
73. To Kill A Mockingbird, Harper Lee
74. Catch-22, Joseph Heller
75. Herzog, Saul Bellow
76. One Hundred Years of Solitude, Gabriel Garcia Marquez
77. Mrs Palfrey at the Claremont, Elizabeth Taylor
78. Tinker Tailor Soldier Spy, John Le Carre
79. Song of Solomon, Toni Morrison
80. The Bottle Factory Outing, Beryl Bainbridge
81. The Executioner's Song, Norman Mailer
82. If on a Winter's Night a Traveller, Italo Calvino
83. A Bend in the River, V. S. Naipaul
84. Waiting for the Barbarians, J.M. Coetzee
85. Housekeeping, Marilynne Robinson
86. Lanark, Alasdair Gray
87. The New York Trilogy, Paul Auster
88. The BFG, Roald Dahl
89. The Periodic Table, Primo Levi
90. Money, Martin Amis
91. An Artist of the Floating World, Kazuo Ishiguro
92. Oscar And Lucinda, Peter Carey
93. The Book of Laughter and Forgetting, Milan Kundera
94. Haroun and the Sea af Stories, Salman Rushdie
95. La Confidential, James Ellroy
96. Wise Children, Angela Carter
97. Atonement, Ian McEwan
98. Northern Lights, Philip Pullman
99. American Pastoral, Philip Roth
100. Austerlitz, W. G. Sebald
Authors who probably should be on the list but aren't: Walpole, Zola, Smollett, Chesterton, Scott, Hugo, maybe Burney, Powell, (Dance to the Music of Time was started before my 50-year cut-off).