Folkiedave has it right in the study I have mentioned. Those who knew they had been prayed for had a statistically significant worse outcome than the other two groups (mind: with large numbers involved a statistically significant effect can be fairly small). This is not the first result of this kind (another is mentioned in the link below).

This could be a nocebo effect ("My God, they assign me to the group who is prayed for: Is it really so bad"). The authors of the study report it but treat it as a statistical fluke.

I do not think the effect of prayer could or should be studied for several reasons:
(1) If there is a God, why should he be forced to interfere by prayer that is randomly assigned in a study?
(2) "Study prayer" comes only in addition to genuine prayer by friends and relations. A real no-prayer control group ("please tell all your friend and relations not to pray for your recovery, because you are in the no-prayer at all control group") will never be run for obvious reasons.
(3) The causal relation I-pray-and-therefore-I-get is not really a Christian idea (Ebbie has said that I think). To pray for something/someone with all your heart with no good result (missing child found dead) is never treated in Christian teaching as a proof for the absence of a God.

The article below mentions some of the problems with prayer studies. My opinion is found among the arguments against such studies. But I know that there is a subgroup fo Christians (in particular in the USA) who list seeing positive effects of prayer as a proof of God. For such a simple-minded thinking it is worthwhile listing methodological problems and pointing to other studies.

When my daughter was 7 years old, she came to me and told me she could prove there was no God. How, I did ask. She said she'd pray for X (her most hated classmate) to break a leg and if he would not break a leg that would be the proof of there being no God. I sighed, praised her for the methodological thinking but told her that if there was a God he'd surely not listen to prayers praying for bad luck of others.

She hates going to religious instruction in school but her parents (both atheists) think she has to be somewhat older before deciding on her own that she does not want to hear about God and religion (it is optional).

In summary, I find prayer studies pointless, but I like to list methodological problems and other finding for those who believe in such studies.

Can Prayers Heal? Critics Say Studies Go Past Science's Reach

Studies about placebo effects, that's something different. If only these effects were not so weak as they are and if they would show not only in subjective outcome variables...

Wolfgang