I've used ASUS motherboards a lot and have always had good luck with them.
Typically, if you order from places such as NewEgg, you can check out the customer comments to see how well they work with linux. (always seem to be some comments regarding linux)
Lately, I've been buying Dell desktops as they have some incredibly great deals. (my VM server is a quad-core (intel core2quad) system with 6GB of ram and I got that system from Best Buy for under $700) No problems whatsoever with linux.