Alister McGrath is a Ph.D. in Biophysics from Oxford who turned around and became a top historian of the Reformation. He is also a former atheist. His latest book, The Twilight of Atheism, takes atheism on from a very respectful vantage point and deals very effectively with its claims. I read the book and enjoyed it thoroughly. I've moved on to his Dawkin's God, Genes, and Memes.
Happily, he's excerpted Twilight for Christianity Today's web site. Here's a bit:
Atheism was once new, exciting, and liberating, and for those reasons held to be devoid of the vices of the faiths it displaced. With time, it turned out to have just as many frauds, psychopaths, and careerists as religion does. Many have now concluded that these personality types are endemic to all human groups, rather than being the peculiar preserve of religious folks. With Stalin and Madalyn Murray O'Hair, atheism seems to have ended up mimicking the vices of the Spanish Inquisition and the worst televangelists, respectively.
One of the most important criticisms that Sigmund Freud directed against religion was that it encourages unhealthy and dysfunctional outlooks on life. Having dismissed religion as an illusion, Freud went on to argue that it is a negative factor in personal development. At times, Freud's influence has been such that the elimination of a person's religious beliefs has been seen as a precondition for mental health.
Freud is now a fallen idol, the fall having been all the heavier for its postponement. There is now growing awareness of the importance of spirituality in health care, both as a positive factor in relation to well-being and as an issue to which patients have a right. The "Spirituality and Healing in Medicine" conference sponsored by Harvard Medical School in 1998 brought reports that 86 percent of Americans as a whole, 99 percent of family physicians, and 94 percent of hmo professionals believe that prayer, meditation, and other spiritual and religious practices exercise a major positive role within the healing process.