As someone who has literally read thousands of fantasy and sci-fi books(at least up in the one thousand and more), my favorite book is still a bit of pulpy action/horror b-movie style fun named Monster Hunter International, by Larry Correia.
For a more serious, and thought provoking series of good literature, I'll probably have to give the award to Tale of the Malazans: Book of the Fallen by Steven Eriksson.
That said it's tough to to really single out the best when you've gone through as many books as I have, especially since it spans a reading period of more than 20 years, and my own knowledge, maturity and taste has changed.
I mean I remember reading Isaac Asimov's entire sci-fi collection of interconnected series and stories as a teenager and liked it because it was so thought provoking, but it's not exactly rivetting literature, it's quite dry, and I'd probably find it boring now. Some books and series I've read I'm afraid to return to in case it breaks the magic, like Robert A Heinlein, William Gibson, Ursula Le Guin or Tracy Hickman and Margaret Weis.
I'll throw out some of my favorite authors, aside from above mentioned: George RR Martin, Alastair Reynolds, Ian M Banks, Robbin Hobb, Peter F Hamilton, Peter Watts, Vernor Vinge, Lois McMaster Bujold, Dan Simmons, Raymond E Feist, L E Modesitt jr, JV Jones, Trudi Canavan, Frank Herbert, Greg Bear, Terry Pratchet, Gene Wolfe, Karen Miller, Marko Kloos, Peter Grant, Brian Aldiss, Conn Iggulden, William Duggan, C S Friedman, Charles Stross, Kurt Vonnegut, Douglas Adams, Neal Stephenson, Neil Gaiman, Larry Niven, John Birmingham, Jim Butcher, Mary Doria Russel, Aldous Huxley. I could go on but I ran out of steam a bit.