Epiphenomenalism tries to reduce mental activity or consciousness to physics somewhere in the body. I agree with William James in rejecting this position. The body is something we play like an instrument. It does not play us. This is especially evident since neuroplasticity has replaced the idea of the brain as a static organ:
http://en.wikipedia.org/wiki/Neuroplasticity
I was reading Thomas Nagel's
Mortal Questions recently where he has a chapter on panpsychism. He provides an example of the difficulty of trying to maintain an emergent form of epiphenominalism.
Panpsychism is the view that everything is in some way conscious. Now Nagel is not a theist (to my knowledge) nor a new age psychic. His problem is essentially how can one maintain a materialist reductionist view and also allow consciousness to emergence as something new even as an epiphenomenon. If everything can be reduced to physical properties, if physics is causally closed, those mental properties must be reduced as well. Since he doesn't believe in a soul of any sort, those mental properties must be in all matter, hence panpsychism.
This pushes consciousness down to the subatomic level (and might incidentally explain some of the indeterminism there if his view is correct). However, what is worse for a materialist position, because of the evidence for the big bang, this also pushes conscious right outside of space and time to exist along with whatever quantum "field" might have been present to start our universe. At this point I don't see any difference between his view and some theisms.