Another big one is Frank Herbert's Dune, which is usually on the short list for best Science Fiction novels ever. Also, Cat's Cradle by Kurt Vonnegut.
You are right that Dickens has the most with nine. Next are Graham Greene and Evelyn Waugh with eight each. I suppose Balzac has over 100 items on the list since the author included the La Comedie Humaine.
I don't know if these deserve to be in the top 1000 but they are prominent enough that I looked for them:
Watership Down by Richard Adams
The Moon is a Harsh Mistress by Robert Heinlein
Roots by Alex Haley
If on a Winters Night a Traveller by Italo Calvino
Sometimes a Great Notion by Ken Kesey