Nancy recently blogged about Harry Potter and the whole "christian" hullaballooo about it, which seems to have died out since the days of the early books. I highly reccommend her post.
And, in the comments, "The Golden Compass" came up. I saw a preview for the movie when I went to see the last Harry Potter one.
A friend had recomended the book as I was reading the first Harry Potter - as somehow similar, but better. I suppose they're similar in that their protagonists are 12 years old, and they're fantasy, and maybe that they're about good and evil, but very different books.
Someone commenting on Nancy's blog remarked that this movie would create more of a stir, as the author is not a christian, and the story is most clearly anti-church.
I doubt it, partly because it's a much less popular series, partly because it's MUCH more likely to be too hard to read for many kids (I can't imagine anyone under ten, or maybe 14, being able to get through it)
It really helped explain some things, when I first read it. Things I already knew, but didn't know how to say to other people. There's a definite theme of there being something beyond our current understanding, but organized religion has it ALL wrong, and in a really dangerous way.
I highly recommend the series ("His Dark Materials") I'm re-reading them at the moment (third time, I think) and am, yet again, a bit blown away.