In Theory, the CPU is the hotest component and needs the best cooling, so it is first in line. NB while is questionable if really needs cooling, is kind of a builders choice. W/C the NB for silent running or use the fan that came on it. Either way on most MB's the NB doesnt really get hot enough to make a noticeable differance in water temp. My self W/C for silence mainly so I W/C the NB and The GPU. If it makes my system more stable and I can get a few more FPS's out of it GREAT, if not still great, one less fan howling at me.
It seems to me with the rash of video cards this past year, the GPU should be more of a concern about heat than the NB, I W/C both and cover my arse
Aardil