In his 1993 book, Warrant and Proper Function, Dr. Alvin Plantinga argued that we as humans cannot truly possess knowledge unless our cognitive faculties function properly, but there is little reason to believe that naturalism can produce proper functioning cognitive faculties.
In the final chapter of the book, titled, "Is Naturalism Irrational?", Plantinga presents his Evolutionary Argument Against Naturalism (EAAN), a summary of which can be found here, where he argues that it is irrational to believe in both naturalism and evolution. This is because the probability of our cognitive faculties being reliable, given naturalism and evolution, would be fairly low since they were produced by processes which were not aimed at producing true beliefs, but at survival and propagation. This defeater for the reliability of our faculties provides a defeater for belief in naturalism itself.
At the 2010 Evangelical Philosophical Society's Apologetics Conference, Dr. Angus Menuge spoke on the subject, "Reason Cannot be Located in a Materialist World" where he gave a number of arguments against naturalism's ability to meet the requirements for reasoning to take place. Wintery Knight has an excellent post with links to Dr. Menuge's paper, a copy of his PowerPoint presentation, and a link to where an mp3 of the presentation can be purchased.
For some time now, I have been compiling a list of things which atheists must believe, can't believe, or can't account for, all of which comprise an argument that atheism is irrational. (I realize that not all atheists are naturalists, but for my current purposes, I will use the terms atheist, naturalist, and materialist interchangeably.)
The atheist must believe...
• that many things we sense to exist, such as the mind, are illusions
• that strictly natural processes, including random mutations, can account for the appearance of design in nature
• that complex specified information can arise from matter and does not require an intelligent cause
• that life can come from non-life
• that the objective moral values and duties we perceive are merely human conventions
• that there is, therefore, nothing objectively wrong with murder, rape, child molestation, genocide, racism, etc.
• that some form of determinism is true
• that something can come from absolutely nothing or that matter and energy are eternal
The atheist cannot believe in...
• free will
• the existence of any ultimate meaning or purpose to life
• the existence of objective moral values or duties
• the existence of any moral facts
• the inherent dignity or value human beings
The atheist cannot account for...
• human reasoning
• human knowledge
• universal laws of logic
• the uniformity of nature
• the fine tuning of the universe for intelligent life
• why anything at all exists rather than nothing
• the truth of anything
Note that nothing in this last section is meant to imply that atheists can't reason, use logic, or prove the truth of propositions. He simply cannot provide any grounding for these things unless he borrows tools from the theist's toolbox.
Finally, the atheist must believe in naturalism even though there are defeaters for the belief in naturalism itself.