Really depends on the purpose of the system.
Generally it's true if you are going to spend in the $200 or higher range, for a CPU, you're willing to budget more for extra CPU performance and will likely be buying an Intel. The vast majority of all dedicated workstations fall into this category because of this.
If it's just for gaming, general purpose use, or even most typical home uses including photo and video editing work, nothing wrong with saving some money on an AMD CPU/chipset.
All three of the computers I currently use are Intel based systems (core quad/nvidia, core duo/ATI, core duo/nvidia). When I build a dedicated Maya workstation, it will be another Intel system based on 1366/i7, most likely ATI video unless Fermi significantly changes the performance playing field.