Aaahhh My field of expertise, ... sorta.
Here's the scoop of the poop. Intel has taken the lead for the better processor for quite some time. However, both Intel and AMD have their own niche. Intel is designed mainly for workstations where AMD is designed more for the gamers and hardcore enthusiasts. Intel, when they create their chips, have always pushed the chip to the limit of stability and labeled their processor at that speed. AMD has always labeled their processors a bit slower than the maximum stability. Intel is not very good for overclocking, stability issues mainly. AMD, who has designed their chip for the hardcore enthusiast, has great overclocking abilities. Intels chip is designed more towards a workstation and works great for CAD, Photoshop and other processor intense applications that use math quite a bit. AMD, better for gaming and other not-so-intensive math, but more intense graphics.
So, If you looking for a Workhorse, CAD machine type of system, go with the Intel and a good Graphics card.
My vote is the Intel.