I'll second the recommendation for Lynch, although I've only read the first book in the series so far. Rothfuss was also pretty good but he needs to finish the damn sequels already. It's been what, three years? And they were supposed to be a book each year. Granted he seems to be polishing them up to respond to the few criticisms people had of the original book, and apparently he had a loss in the family that resulted in the loss of a lot of his time, but that doesn't explain the entire delay.
You might also like Ursula K. LeGuin and John Twelve Hawks; I wrote a mini-review of the latter's first book (which I'm halfway through)
here.
I also liked Steven Erikson's first book but got interrupted halfway through the second one due to school a few years ago and haven't picked the series back up since. I plan to restart it after I finish off some of the other books I'm in the middle of.
And he's not really sci-fi (although he is influenced by it) but I always tell people to read Thomas Pynchon.
Gravity's Rainbow is too much to start out with (although it's generally regarded as his best) so I'd say go for one of the shorter books;
The Crying of Lot 49 or
Inherent Vice, or maybe
Vineland.
Vineland has ninjas. You can't go wrong with ninjas.