Amd or Intel, it doesn't really matter. Both systems are going to be fast as hell and you won't notice the difference between the two.
What is more important than the processor ( amd or intel ) on the over all performance of the system usually boils down to the supporting chipset and associated peripherals. Nothing worse than having a crappy integrated NIC or sound card with equally crappy resource hogging driver bogging down your machine and making it unstable. And this is an extra concern when it comes to building a linux box.
Me, i'd go the intel route and run uae on windows.
