OK looks like the list is officially closed to voting, but as the thread is still open and people are adding their votes, I figure I'll add mine:
New nominations:
Epic of Gilgamesh, author unknown, fantasy. Why should it make the list? Because it's the earliest known written story and as such, it is the first to delve into themes and elements of fantasy and heroism.
The Time Traveler's Wife, Audrey Niffenegger, 2003. Why should it make the list? Because it's not squarely SFF, which I think this list (which is supposed to be a tool for writers, after all) could use to expand writers' horizons and conceptions of their genre.
A Clockwork Orange, Anthony Burgess, 1962. Why should it make the list? Because it's a classic (and exists on lots of "Top X" book lists) and involves a gritty dystopia, an anti-hero, and an examination of free will.
Throwing in my votes:
Ender’s Game
Dune
Harry Potter
Lord of the Rings
Chronicles of Narnia
Brave New World
1984
The Odyssey
A Midsummer Night’s Dream
The Handmaid’s Tale
Snow Crash
The Forever War
Hitchhikers’ Guide to the Galaxy
A Song of Ice and Fire
Kingkiller Chronicle
The Stand
Slaughterhouse 5
Farenheit 451
A Canticle for Leibowitz
A Wrinkle in Time
Flowers for Algernon
Never Let Me Go