Here are some of my picks:
Way Station by Clifford D. Simak
Time is the Simplest Thing by Clifford D. Simak
Native Tongue by Suzette Haden Elgin
Gibbon's Decline and Fall by Sheri Tepper
Grass by Sheri Tepper
Where Late The Sweet Birds Sang by Kate Wilhelm
The Dispossessed by Ursula Le Guin
If Zenna Henderson's work weren't collections of short stories I'd include her stories about "The People." Check out the compilation "Ingathering."
Andre Norton has had such a prolific career it's difficult to know what to pick. I'm sure almost everyone has a favorite. I remember the haunting Moon of Three Rings which I read in grade school and again a few years ago.
Some of James Tiptree Jr/Alice Sheldon's best work is also short stories and novelettes. I loved Houston, Houston, Do You Read? The Women Men Don't See is another excellent Tiptree story.
Joanna Russ should definitely be in such a list for The Female Man You may remember that a precursor to this book was the short story When It Changed, first published in Harlan Ellison's Dangerous Visions. There is, of course, a theme that relates from James Tiptree Jr's Houston story. But is it so odd that more than one woman writing science fiction should think to question what life might be like without men? I see this less as wish fulfillment than a thought experiment to figure out who we are when we are not expected to fill a particular role.
Another surprise was the absence of Lloyd Biggle Jr. from the list. Perhaps he would make the top 100, I don't know, but he's definitely in my top 50. As for which book, I hardly know where to start. I grew up reading his books over and over again. All The Colors of Darkness or The Still, Small Voice of Trumpets, perhaps.
In fantasy, I am amazed the list did not include one book from the prolific and excellent Charles de Lint. Again, I almost don't know where to start. The Onion Girl is excellent, as well as Trader. His linked short story collections are also really powerful. I particularly enjoy all of his stories and books set in Newford, which I feel is like a second home, I've visited so often. Memory and Dream is an early Newford book that sets the stage for so much that is to follow. For a complete list, check out his Wiki page.
Also in fantasy, I've been very fond of Tea With The Black Dragon by R.A. MacAvoy. At the time I remember that I thought it was a unique use of a mythological creature that wasn't a fairy, vampire, or werewolf. The story was equally creative.
The Mirror of Her Dreams and A Man Rides Through were books I enjoyed more than the author's Thomas Covenant books.
When it comes to Heinlein, having grown up on his books I found I wanted to add titles. Though frankly I was never a fan of Starship Troopers. I found it odd that The Moon is a Harsh Mistress or The Number of the Beast didn't make the list.
I was surprised that Larry Niven and Jerry Pournelle's The Mote in God's Eye didn't make the cut.
Octavia Butler's novel Kindred ought to be on any "best of" list. I personally like Survivor although I acknowledge that the writing wasn't as technically good as in some of her other works. The story "Bloodchild" is a powerful example of the dilemmas she introduces to her human characters.
Roger Zelazny has written so many that I can imagine it was hard to choose. Lord of Light is one of my favorites and I thought it too dense when I read it as a child--much of it was over my head. Then we had to read Siddhartha for school and when I went back to Lord of Light it made a lot more sense. Like most Zelazny fans, I devoured the Amber series. I also enjoy Eye of Cat.
Then there's Spider Robinson, who coined the phrase "God is an iron." I'd want to put Mindkiller and Stardance in any top sci fi/fantasy list.
I would put Theodore Sturgeon's Godbody on the "best of" list. He also has an excellent story in Dangerous Visions.
Also check out John Brunner's The Crucible of Time.
Chocky by John Wyndham, a book about a child's encounter with an alien consciousness, the film rights of which has been acquired by Steven Spielberg, is the second science fiction book I ever read. I still remember it fondly. It was also turned into a children's TV show in the UK.
Chocky via BBC radio: http://www.archive.org/download/otr_chockyjohnwyndham/1967-Xx-Xx_Xxxx_-_Chocky_-_John_Wyndham_-_1967_0001.mp3
Other authors I'd prefer to see represented: Lois McMaster Bujold, Steven Brust (Jhereg novels), Steven R. Boyett (Ariel), Jack Finney (Time and Again, The Body Snatchers), Gordon Dickson (Tactics of Mistake) (short story Danger--Human), Alan E. Nourse, Katherine Kurtz, Anthony Boucher, Fritz Leiber (Conjure Wife, Gather Darkness, Fafhrd and the Gray Mouser stories, Gonna Roll The Bones), Robert Sheckley (Mindswap), Katherine Kurtz (Deryni books), and Sharon Shinn (The Shape Changer's Wife), Louis Charbonneau (No Place On Earth). I'm also in love with Anne McCaffrey's "Ship Who Sang" stories among others.
Do you have any favorite sci fi/fantasy books you'd like to add? I'm sure I'll think of many more over time.