You'll find that for "most" users, they would not see a difference running the types of apps that most users run. Hardware can be like politics, people have their opinions and they can be hard to change. If these computers are for general use, then either platform will do just fine.
Is there any centralised information on which motherboards work best with modern Linux. Date of question:- 20th August 2012.
The question also includes motherboard bundles and graphics cards.