There is a must-read paper in Nature about the limits of functional MRI as an experimental tool by one of its pioneers, Nikos Logothetis. (Also discussed by Jonah and Vaughan.)
This paper is pretty technical, but Logothetis hits the important points of what it is we think we are actually measuring using the fMRI. Also, he notes that the difficulty in interpreting fMRI data lies in the fact that you have to make assumptions about network architecture that may or may not be...