Research into the impact of prayer on patients undergoing heart surgery has found no discernible benefit (Benson & Dusek et al. 2006, reported in Science & Technology News).
This work looked at the effect on the ‘prayee’. While there were no benefits there, I think that there are likely to be demonstrable impacts on the ‘prayor’.
Prayer that asks for something good for someone else (intercession, metta) reminds me of mirror neurons. It seems that doing something, and watching someone doing something, both activate the same brain region; at some level we don’t distinguish between doing, thinking, and watching.
I suspect that intercessory prayer activates the “handing stuff over” center in the brain. The metaphors we use when talking about generous acts provide some support for this guess. For example: “Give her my best wishes,” “He extended his sympathy,” and “My heart went out to him.” One could test this by measuring the activation of mirror neurons in humans while praying, and comparing it with activation when giving something, or watching a gift.
Doing good makes us feel good, and if the mirror neuron hypothesis is sound, thinking about doing good is almost as good as doing it. This suggests that intercessory prayer should activate both mirror neurons for motor activity, and brain centers for emotional well-being.