No Life is Good by David Benatar
This is an article written by David Benatar which argues that all human life, by nature, is not good by virtue of the fact that life could be so much better. Since life could be so much better than it is, comparatively, human life is not good. At least that's how I remember it, I link it here mostly for egotistical reasons, I ended up having a very interesting discussion with an anti-natalist named Rob in the comment section.
Nonoverlapping Magisteria by Stephen Jay Gould
I don't think it would be unreasonable to say that the main target of the New Atheist's criticism is the ideas contained in this essay. Gould argues that science and faith have separate domains, or, magisteria. They are separate methods that deal with separate issues, and consequently, there is no conflict between science and faith so long as they remain is their proper magisteria. I am not entirely sure where I stand concerning this argument, it's my goal to eventually one day write something on here exploring it.