i dont like paralle setups because some times you can get dead spots where there is verry little water flow, ie all the water will follow just one path.
i also like the top setup, because you have the CPU right after the rad, and in my experiance this is the best way to cool. but i would add a larger res to the system, i found that mine cooled the best with at least 1.5 gallons of water.
with .75 gallons of water in my p4 wc @ 2.8oc, folding 24/7 temps stabalise at 33c, after 14 hours
with 1.5 gallons of water in my p4 wc @ 2.8oc, folding 24/7 temps stabalise at 31c after 58 hours
with 3 gallons of water in my p4 wc @ 2.8oc, folding 24/7 temps stabalise at 31c after 92 hours
all temps taken with the asus probe, and at 1 week or 168 hours. of running 24/7 with only folding and winxp pro running.
i also noticed a 2c drop in CPU temp when i moved the GPU from befor the CPU to after it in the closed water loop.