I have been building computers since the 80-286sx processor that ran at a whopping 15mhz. I now have a pocket calculator that has more speed, power, and memory. I have used about every processor you can imagine, and swapped quite a few around. In all that time, AMD had kicked all kinds of ass, IF you knew how to overclock and cool your system. Intel is not designed for overclocking at all ever. Amd designs great processors, but does not put as much money into R&D as Intel does. There is no way they can match the budget. They are simply not as fast on the uptake as Intel is except in their server division. Their servers are better on the whole than any comperable Intel system.
That said, Sun makes a hellafuck processor called the Spark. Their servers are the stuff of legend, and they design super computers for the likes of NSA's code crackers, and the DOD's DARPA. These things are truely scary in what they can do. They have a server that has 256 2.8ghz processors, 512gb ram, and enough HDD space to store every scrap or written literature since the dawn of man.
And this is not even a custom system! Their high end systems run upwards of a million dollars a pop, and have up to a 256 bit processor. Just recently they started to get into making desktop systems, but I have yet to get to try one.

Oh well, I will end up with one eventually.
My vote:
AMD, unless a SPARK is available.