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Like my previous reading list, I recognize that not everyone is going to want to read all of these. Therefore, I'll try to give you some information about what I am recommending to help you choose. Although I am not intentionally using the word "intermediate" to reflect increased difficulty as much as I am to indicate that most of these books probably aren't your best starting points to learn about atheism, it is true that a couple of them are somewhat more challenging reads than most of what was on the introductory list.
Introduction to Intermediate Atheism
We have to resume our study of atheism somewhere, and few books provide a better overview than The Portable Atheist: Essential Readings for the Nonbeliever
Philosophical Atheism
There are so many excellent possibilities in this area that it is tough to know where to start. However, given theists' obsession with viewing atheists as morally deficient, it probably makes the most sense to focus there. For those with a particular interest in the question of whether we can be good without gods, Richard Carrier's Sense & Goodness Without God: A Defense of Metaphysical Naturalism
If increasingly complicated philosophical arguments do not deter you, also consider Michael Onfray's Atheist Manifesto: The Case Against Christianity, Judaism, and Islam.
Scientific Atheism
In my Atheism 101 reading list, I recommended that everyone start with one of my personal favorites, Carl Sagan's The Demon-Haunted World: Science as a Candle in the Dark. Just thinking about this one makes me want to go back and read it again! If you liked it and are ready to pursue scientific atheism, consider Michael Shermer as an excellent next step. Start with Why People Believe Weird Things: Pseudoscience, Superstition, and Other Confusions of Our Time
Should you find Shermer a little too basic, which you might if you have a few college-level science courses under your belt, consider Victor J. Stenger's God: The Failed Hypothesis. How Science Shows That God Does Not Exist
Explaining Religion
For those interested in better understanding why and how religion came to be, I have two recommendations: Daniel Dennet's Breaking the Spell: Religion as a Natural Phenomenon
Another book I'll place in this category that I cannot recommend highly enough is Earl Doherty's The Jesus Puzzle: Did Christianity Begin with a Mythical Christ? Challenging the Existence of an Historical Jesus
Society, Culture, and Politics
Some of what you'll find in this section is a bit dated since it focus on the period of time during which we in the U.S. were under the thumb of the Bush regime. Still, there are many excellent books here that help to demonstrate the perils of mixing religion and politics. One of the easier and more compelling reads is John Bice's A 21st Century Rationalist in Medieval America: Essays on Religion, Science, Morality, and the Bush Administration
You may also want to check out Christopher Hitchens' God Is Not Great: How Religion Poisons Everything in this category. Of the books written by the big-name atheist authors, this one is probably my least favorite. However, Hitchens really is a talented writer who deserves to be read.
If you are up for something completely different that is virtually guaranteed to leave an emotional impact, Ayaan Hirsi Ali's Infidel
If you think I've missed any good ones (and I'm sure I have), please feel free to recommend them in the comments section. Of course, please understand that recommending books that you personally wrote is unlikely to be taken as seriously as recommendations from impartial readers.