Evolutionary explanations of human mind and behavior
It seems these days there are many bold folks out there who go so far as to say that human beings evolved to be religious. This is sometimes used in discussions with theists as undermining the ability of a religious impulse to be evidence of god(s). While I agree with the basic idea here, I would urge caution with these claims, because if the believer argues that we don't have direct evidence for this, they would be right. An evolutionary explanation of religion would need evidence that religion has a direct benefit to survival and/or reproduction, and it seems that the balance of evidence shows the opposite - namely, that religion does more harm than good to its adherents and cannot have directly evolved. We can of course posit that religion is more of an epiphenomenon that simply is a byproduct of the interaction of distinct impulses, each of which is independently an evolutionary advantage in and of itself, thus allowing for an evolutionary explanation of religiosity. For instance, the fear of death, social imagination, and the need for something which acts as "social glue" holding communities together. Each of these by itself is evolutionarily advantageous (thus allowing for an evolutionary explanation) and their complex interactions taken together foster the development of religion, even if religion is not advantageous.
The brain is molded by experience, especially the evolutionarily more recent neocortex. How can evolution, which can only operate within the domain of what is determined by genetics, explain the functions of the brain? There don't seem to be any genes in the human genome that directly code for differences in neuron function that would account , for instance, for why one part of the brain is responsible for spatial perception, another for social planning, another for recognizing sounds, another for controlling the recall of memories, another for appreciating humor, etc. Rather, this all seems to emerge from plasticity and a bunch of neurons that start out essentially identical to each other in structure and function. Thus, even though we as atheists can all agree "Goddidit" has no explanatory power, I think we need to remain humble about using evolution as an explanation for the intricacies of thought and behavior. On the flip side, though, this makes arguments such as Alvin Plantinga's EAAN easier to demolish - simply by pointing out that evolution does not select beliefs or desires in the first place, and rationality and intelligence are explained by the dynamics of neural networks in general, not evolution (except insofar as the latter was necessary for neurons to develop in the first place).
I think it also raises the question of human uniqueness to a new level. Many traits that are often claimed to be distinctly human lead to interesting questions in the context of evolution and neuroscience, such as abstract thought, self-reflection, cultural symbolism, and morality. If evolution (or indeed, genetics) doesn't explain these things by itself, we have less of a reason to think other animals don't have them as well, even if due to their lack of language they don't manifest as obviously in those animals as in humans. And this (in obvious ways) poses problems for a lot of religious beliefs that must regard humans as distinct from other species due to these traits. But it also makes it seem totally unjustified to regard our species as apart from nature. (For instance, the very use of the words "natural" and "artificial", and claiming we are "fighting our instincts" in the context of morality, as though a distinction between instinct and moral rationality exists in the first place...). I am raising this issue in part because it is interesting, but also because I have actually seen theists use them as arguments that no one really believes that naturalism is true!