Bump for Borneman's book. It's a great coral primer. I hear "The Book of Coral Propagation Volume I" by Anthony Calfo is a great read, too. I haven't picked that one up yet but plan to.
Also, Reef Invertebrates by Calfo and Fenner has a great chunk (about the first 1/3 of it) on more scientific aspects of the tank and modern methodologies. Even if you're not that into inverts I found it really helpful.
I was talking to Jeff at JL a while back and he said the Baensch atlas is fairly good, but the information has gotten somewhat dated. He didn't seem a big fan and after flipping through them at work I kind of see where he's coming from. They're a great quick reference and give a good rundown for species, but not that pleasant to actually sit down and read.
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