I don't know if it'd really be Sci-Fi, but Phillip Pullman's His Dark Materials trilogy is awesome. I think it's generally considered fantasy, but it does deal with some sci-fi concepts like dark matter, parallel realities, and features some steampunkish tech in one of the worlds.
It even features in Trek literature: in Children of the Storm, when the crew of the Demeter discuss how to insert O'Connell's seeds into the bubbles of the Children of the Storm, the "ancient myth" of the subtle knife is brought up.