1. The Lord Of The Rings Trilogy, by J.R.R. Tolkien: I think I would have been very surprised if this had been anything else. I used to listen to WXPN, a college station out of Philly, and after they had their fundraisers, they would have the countdown. Since they broadcast at 88.5, their countdowns were always the top 885 artists/albums/songs, and it was usually pretty meaningless, because a list that big is too large to have any kind of meaning, and you knew the top three was going to be either Beatles/Dylan/Stones or Beatles/Stones/Dylan. But it probably deserves the slot. It's been hugely influential on almost everything in fantasy that came afterwards. If a fantasy series wasn't emulating LotR, then it was deliberately subverting elements of it.
2. The Hitchhiker's Guide To The Galaxy, by Douglas Adams: This has had a lot of different incarnations, radio plays, novels, TV series. I remember the old Infocom computer game, which I played after I had read the Restaurant at the End of the Universe, but before I had read Hitchhiker's itself. It's also been hugely influential on geek culture, with many of us answering "42" when asked for a random number.
3. Ender's Game, by Orson Scott Card: I know this was influential on a lot of science fiction fans because it was the first juvenile genre work not to talk down to kids. I only encountered it as an adult, and I think it's pretty decent, but I don'y have the nostalgic connection to it that a lot of fans do.
4. The Dune Chronicles, by Frank Herbert: I love Dune. I wrote a post on my top 10 favorite Dune characters at my old blog. I even like the Heretics/Chapterhouse cycle. I like Dune but I'm surprised that other people do. I think it's a very, very good book, but not something that would have broad appeal. It's dry, it's difficult and though it's been consistently ranked as one of the best science fiction novels ever, I don't know that many people who actually like it. I guess they're out there (somebody must be buying those dreadful prequels), but it doesn't seem to have the same following as other SF classics. I think we're starting to see here is people voting on how they want to be perceived, rather than what they actually like.
5. A Song Of Ice And Fire Series, by George R. R. Martin: I like the first three books, tolerated the fourth and haven't yet read the fifth. One thing I'll say is that Martin advanced the plot in every chapter. There was no filler. They are these huge bricks of books and he still managed to have something happen in every chapter. That's pretty impressive. That said, I think the ranking is somewhat inflated by the new book release and the HBO series.
6. 1984, by George Orwell: Influential, a cultural touchstone, but again, I think we're getting into people voting on the reputation of the book and not their personal opinion of it.
7. Fahrenheit 451, by Ray Bradbury: See comments for 6
8. The Foundation Trilogy, by Isaac Asimov: See comments for 7
9. Brave New World, by Aldous Huxley: See comments for 8
10. American Gods, by Neil Gaiman: Probably my favorite work by Gaiman, and that's including the Sandman. The culmination of his work bringing myths to life. I'm not sure it's the 10th best Fantasy book ever written though.
Other commentary. Lord of Light didn't break the top 100, and, on reflection, that's not hugely surprisingly, because it's not as accessible as some of the other works on the list. It'a galling, though, that such stinkers beat out the Amber books. The Wheel of Time at number 12?! Jesus. The Sword of Truth at number 62 instead of a compost heap?! That's a crime, man! The Sword of Shannara over both Elric AND Conan?!
Heh. I'm reminded of one of the afterwards from an author of one of the stories in Lord of the Fantastic (I forget who, exactly) who notes that all these authors have so many dedicated fans who know nothing about the interests of other fans. So while I'm bemoaning the fact that Lord of Light didn't make the top 100, someone else out there in the internet is no doubt complaining that it was nominated at all.