If you are just doing GPU mining then I'd say go with AMD. The CPU is cheaper and the motherboards (in my experience) tend to be cheaper as well. They also tend to have a easier upgrade path, if you want to upgrade the CPU for an Intel based machine you typically will need to replace the motherboard, with AMD they usually have the same socket for several generations.
Thanks, I didn't know that about AMD boards. My long term strategy is start with maybe a duel core cpu, and upgrade it to a quad or 6 core later on after the GPU's start making a profit, then hook an external ASIC with it's own PSU up and mining Sha-256 with the idle (for the most part) CPU.
End result is the whole system will be under quite a bit of stress. Water cooling is probably an option at that point. So Reliability is real important to me.
