One of my favorite atheist writers is Massimo Pigliucci, his blog is Rationally Speaking. He doesn't write often but when he does it's always worth a read. What he has on today's blog is a list of must read books.
This is his list of Top Ten books on Evolution.
And this is his Top Ten for Philosophy.
This is on Amazon with a note from Massimo on each book. I have to admit I haven't read even one of these, but I've heard about most of them, read parts of them and read people talking about them. It seems odd that a defender of evolution such as myself, with a better than average knowledge of the subject has never read Origin of Species by Darwin. When it comes to scientific stuff I prefer magazine articles, entire books can be very daunting, plus I know that many things have changed in evolutionary science since Darwin's day so I tend to think it's better to read more modern things.