The first is God on Trial: Dispatches from America's Religious Battlefields, by Peter Irons. Ed Brayton recommended this one, and I have to say, it was quite fantastic. It's a summary of some recent church-state separation cases, featuring detailed analysis of the cases as well as interviews with some lead players. It also has a good overview of the precedent surrounding the establishment clause from historical and judicial perspectives. It's remarkably well-written and thoroughly enjoyable, I highly recommend it.
Next is The Plausibility of Life: Resolving Darwin's Dilemma by Marc Kirschner and John Gerhart. This book is a bit on the technical side, but it really helped my understanding of how life works, to put it bluntly. The authors develop their theory of "facilitated variation", which is essentially the idea that the way organisms develop is highly constrained (and hence basically unchanged across phyla), but this constraint actually allows more variation in body plans: the highly constrained development plan deconstrains development. If you're interested in learning about this kind of thing, it's a very accessible and interesting book.
Now we have Coming to Life: How Genes Drive Development by Christiane Nusslein-Volhard. This book is dense. It's really short but packed with information. Because of that it can be quite hard to read. That said, you probably won't find a better survey of modern evolutionary development. If you're interesting in how you got from an egg and a sperm to a full-grown human, this book is for you.
Finally we have Breaking the Spell: Religion as a Natural Phenomenon by Daniel Dennett. I got this one last year, and never bothered to read it. And honestly, I wasn't missing much. I'm not entirely sure why it's so widely acknowledged, since I have to yet to read a chapter and not wonder, "Did he even say anything during that whole chapter?" I have yet to discover a thesis, and he just mulls around considering hypotheses without actually deciding anything. In other words, it's perfectly obvious that Dennett is a philosopher.
That being said, he does throw out an awful lot of information, and I could just be missing the central driving force (or it just hasn't become apparent to me yet, I haven't finished the book). Dennett is a skilled writer and intensely knowledgeable, so if you're looking for a book that really does attempt to dispassionately investigate religion, buy this book.
That's all for now, but my stock of books is pretty much out, and I'll need more. If you have any recommendations, please leave them in the comments!