The book section of the Guardian Unlimited has a list of top 10 dystopian novels for teenagers. Several are science fiction (not Lord of the Flies or The Dairy of Anne Frank but certainly Children of Men and A Clockwork Orange). Interestingly, the words "science fiction," "speculative fiction," and "fantasy" never appear anywhere on the list. Margaret Atwood would be pleased, as her A Handmaid's Tale is one of the books listed and she always hated people calling it science fiction—not that she ever proposed giving the money back if you bought it in the speculative fiction section.
At a panel at the 2007 World Fantasy Convention one of the panelists (I think it was Sharyn November) mentioned the enduring popularity of anti-authority books with young readers. Her contention was that it was in fact the job of young people to distrust authority. I suppose most of these books would help them do that.