Voting just closed, and it was very very close. Hitchhiker's Guide got 12 votes, and Dune got 14. If any one Herbert voter had got for Douglas Adams instead, the result would have been different (since it would then be a tie, and my vote for Dune would have been cast out).
Passions ran high, and the result may have hinged on the question of if Hitchhiker's Guide to the Galaxy is a proper science fiction novel at all. I think it is. Being funny doesn't discount some pretty good SF ideas - not to mention some fantastic commentary on human nature. But I also think that Dune is in so many ways the ultimate SF novel, the best and most widely regarded the genre has produced. And Dune is officially the favorite SF novel of the Escape Artists boards.