May's recommendation: the His Dark Materials trilogy, by Philip Pullman. Individual titles are The Golden Compass (called Northern Lights in Britain), The Subtle Knife, and The Amber Spyglass.
For all that I have some issues with the way the end works, this is a very interesting trilogy, all the more so because it's theoretically "children's literature." I suppose it is aimed at children, in that it features protagonists who are on that borderline between childhood and adulthood, and the tale is partly about how they make that transition, which is a common subject of that genre. But the issues it tackles are not simple or trivial in the way that so much godawful writing for children is, and that's why this trilogy, like other good "children's literate," holds interests for adult readers as well.
Lemme tell ya -- those conservative religious folk pitching fits about how Harry Potter is a corrupting influence are so barking up the wrong tree. People in Britain are starting to notice this, but in America people seem to still be blinded by the neon lights around Harry Potter, while behind their backs Pullman's trilogy sneaks around and quietly gathers more and more readers. Rowling's work, to those people, is Satanic because it's got magic; how much worse, then, is Pullman's, with its scathing critique of organized religion? I find it interesting that one archbishop in Britain has come out in wholehearted endorsement of the books, because his reading of them interprets it all as, basically, a critique of what's bad about organized religion -- which then becomes a call, in his mind, for improving it, for thinking seriously about religion and what it means and how its structures work, and discarding the parts that are regrettable human fallacy.
Anyway, on to my usual miserable attempt at a plot summary. The Golden Compass starts off in a world rather, but not quite, like ours, where certain semi-magical things appear to work -- I say semi-magical because of the way they get developed later on, which illustrates my wholehearted belief that high-level theoretical physics and magic can be practically the same thing. The most noticeable difference about this world, however, is that everyone in it -- everyone -- has a daemon, a companion spirit that changes shape while the human is a child, but eventually settles down around puberty. In the class I took on fantasy this semester, we had some interesting discussions about the extent to which the daemon is a part of the human, or something separate, and exactly what part the daemon is, if it's the former; it's a nice, meaty question to chew on. Anyway -- back to this supposed plot summary -- the book follows Lyra, a child raised pretty much by academics in Oxford, as, um, weird stuff goes on. No, turns out I can't give a basic summary, even of the beginning, without giving away things I don't want to. I'll say this much: The Subtle Knife picks up a second protagonist, Will, who's from our world, and from there the story goes waltzing through a number of different worlds, some of them populated by beings who are very much unlike humans, while offering some very thought-provoking possibilities for the way in which people (of whatever shape) might live their lives. And, yeah, it's slamming organized religion along the way, and possibly (depending on your point of view) the entire concept of God (this is the bit that archbishop manages to justify, with his reading of the books).
I'm a purist, so I've always hated the fact that Harry Potter and the Philosopher's Stone got re-titled on its way to America, but I like that Northern Lights became The Golden Compass. Because of that, all three books are titled after certain highly important artifacts that appear in the narrative (although the amber spyglass is, to me, not as important and not nearly as cool as the other two). The "golden compass," also called the alethiometer or truth reader, is positively fascinating, especially if you go here, click on the link for "Alethiometer," and then look at the images given there. The layered meanings, going down and down and down pretty much forever, are culturally constructed but by no means less interesting for that, and then when you figure that which meaning is the relevant one varies depending on the situation, and that the symbols are influenced by each other in context, it becomes a very neat little microcosm of the series. Basically, although it's called a truth reader, there is no Truth. There are only truths, situational, contextual, and maybe misinterpreted by the reader.
I could also talk about the role the subtle knife plays, but that would give away too much. So I'll leave it at that for now.