I love a good booklist, if for no other reason than the arguments that ensue. I think that's what lists are for. And with NPR's new Your Picks: 100 Top Science Fiction, Fantasy books I was not disappointed. The trash talk in the comments was delightfully nutty. The best thing is that everyone in the comments is trashing the people who made the list, who are...the same people as the commentors. So you knew it wouldn't be a definitive list anyway.
I went through the comments to create a alternate list, but there weren't that many people who stayed on point. There seemed to be many who think that fantasy and science fiction should be two lists, but then they don't seem to have a problem with them being shelved in the bookstores in that exact fashion. There were many who brought up the lack of Rowling, L'Engle and Pullman but it was clearly stated that they're saving YA for another list. There was grumbling about Ender's Game being YA but that's not how it was originally published.
So once you get over all that stuff, here are the authors most mentioned that did not end up on the list and were missed by more than one or two people.
By far the name most mentioned was Octavia E. Butler, and for good reason, followed by Samuel R. Delany, usually in the same comment.
The next most passionate outpouring was for Harlan Ellison. I think because he's predominately a short story writer and has many books, any votes for him probably got diffused. Right after him would be his friend Robert Silverberg.
There was some moaning about other Philip K. Dick books, but he's on the list so maybe they should have nominated his whole collection instead.
Poul Anderson and Jack Vance and C. J. Cherryh had a number of fans.
The other honorable mentions would go to H. P. Lovecraft, John Brunner, Mary Doria Russell, Alfred Bester, Joanna Russ, Fritz Leiber, Stanislaw Lem, Edgar Rice Burroughs, and E. E. "Doc" Smith.
There. Now you have an alternate list of great writers to check out. Have fun.