I've been meaning to write a web page about the series of studies that seem to indicate that groups of patients receiving prayer get better health outcomes than the control group. It is an interesting series of studies because it illustrates some of the difficulties, even with randomized double blind trials.
It also raises some interesting theological questions, and although I am not an expert on theology, I find those arguments interesting also.
But there is a third line of thought which argues that research in this area is logically flawed. Bob Carroll, author of the Skeptic's Dictionary [BookFinder4U link], says that research should be confined only to processes which obey the natural laws of science.
If prayer works by influencing God to influence the outcome of an experiment, then God can interfere with the laws of nature at any time. If God can interfere with the laws of nature at any time, then no controlled, double-blind study can be sure of the meaning of whatever outcome results. Any result could be the result of direct influence by God. In other words, the assumption the study is based on is self-defeating. No science at all would be possible if God could be interfering with the laws of nature at will. Science requires a backdrop of lawfulness in Nature in order to discover any causal connection between anything and anything else. -- www.skepdic.com/refuge/bunk18.html#prayer
You can find an earlier version of this page on my original website.