It sort of depends on what operating system you are going to put on it.
Win2k (for those who hate DRM and like stability & minimal system resource use): Win2k does not support AMD 64-bit, there was a patch, but MS never released it. it will run with it as a 32-bit processor. if you get a multi-processor system, or a AMD multicore processor, Win2k supports them well but only 32-bit
WinXP (For those who like integrated DRM & Bloat) has a 64-bit version, and supports multicore, if you get XP professional. XP pro even supports multiple processors. So it doesn't really matter, AMD or Intel, as long as you get XP PRO.
VIsta (For those who..ah, forget it, no one with any sense would get Vista by choice).

My choice would be a Multi-processor AMD-64 system; I run Win2k, so I'm missing out on the 64-bit, but I don't have any 64 bit apps anyway. I dual boot Linux Debian with 64-bit support, so would be able to make use of multi-processors and 64-bit in linux.