I’d go for AMD over intel if you’re mainly going to be using linux – that way you can use the 64-bit versions of linux.
I got a motherboard bundle from Novatech[/url] about a year ago with an AMD 890GX chipset mobo, AMD Phenom II X6 1055T Processor, 4Gb RAM, USB 2.0 & a couple of USB 3 ports. I stuck the nVidia GeForce 9500 GT graphics card from my old PC in there and it all works fine. In fact I first booted it up with the HDD with the Ubuntu install that I’d had in my old PC and after about an extra 30secs of thinking it ran with no problems 🙂
I’ve been running Ubuntu 10.4 and Vbox with WinXP on my new hardware without any issues (asides from the usual ones with Windows 🙄 ) as it supports hardware virtulisation.