It depends if you limit it to books that available as ebooks or not, it also depends if you mean SF or SF/F.
Many of the old classics (Zelazny's books for example) aren't available in ebooks yet and they are certainly in the mix for my favorite SF books.
Just books that are available as ebooks and SF rather than SF/F - Certainly Asimov's Foundation trilogy. I would throw in to the mix some of James Hogan's books, especially his early books (The Gentle Giants series). Many of the Pournelle/Niven books such as the previously mentioned Mote in God's Eye. Probably some of David Weber's books (not great literature, but great stories). For the most part, which one is best really depends on what mood I'm in.