Current generation AMD and Intel processors are pretty close in performance, but guessing which will work better involves a complicated mix of both CPU and memory issues. AMD's NUMA architecture does some things better, and Intel's memory access takes a second hit in designs that use FB-DIMMs. But Intel has enough of an advantage on actual CPU performance and CPU caching that current designs are usually faster regardless.
For an interesting look at the low-level details here, the current mainstream parts are compared at http://techreport.com/articles.x/11443/13 and a similar comparison for the just released quad-core Opterons is at http://techreport.com/articles.x/13176/12
Nowadays (mid-2008) Intel vs. AMD is tight enough that in the context of a database application that it shouldn't be a major driver in your purchasing decision process. On a real server, you should be more worried about how good the disk controller is, what the expansion options are there, and relative $/core. In the x86/x64 realm, CPU architecture is not a huge issue right now for most situations where you're running a database.