In a parallel set up, you would get less restrictions. This inturn should give you better flow rates and in some cases better temps.
Also it allows each block to get cool water instead of the 2nd block getting non cool water. But it has been shown that water that comes out of a CPU block only raises maybe .05C so it really does not matter too much.
Parallel is a little harder to pull off, since you must make sure that each line has equal flow, and that is pretty hard. If you pump is of decent strength, (i.e 200+ GPH) then I don't think you need to worry about going to parallel.
P.S. the .05C could actually be .5C, but I'm pretty sure it .05. I'm trying to find the thread.
The even flow is what I was just thinking about. My CPU is like eight inches over the GPU, if I wyed it at a low level gravity would make the GPU get like 75% of the flow. I'd have to wye it as high as possible...
YOu will be better off running SERIES, not parallel. See this: http://www.extrememhz.com/emflag2-6.shtml Running parallel kills the velocity of the water. Water out of CPU1 is only like .5C or less hotter than when it entered, if that. Unless you have a MONGO pump, like an Iwaki or something that does like 1000GPH, Series is definately the way to go.
you can go parrallel, the gpu doesnt need nearly as much water as the cpu so you could make the line going to the gpu maybe 3/8" or smaller and the cpu one 1/2". But like everyone has said, your temps wont change much, if any. Now if you had 3 blocks thin you might want to try something like this.