This really depends heavily on the type of workload that you are dealing with. The big thing with these servers when comparing an AMD option to an Intel option is going to be the initial VALUE compared at the same price point.
Take for instance the HP DL380p G8 servers with a single Intel Xeon six-core 2.3 Ghz processor and 16 GB of RAM. It is about the same cost (slightly more expensive) than the HP DL385p G8 server which comes with two twelve-core 2.6 Ghz processors and 32 GB of RAM. With the AMD option you're even getting both redundant power supplies instead of just a single PSU. That means you are getting a whole lot more processor cores and twice the RAM for about the same cost or even less.
Clock for clock the Intel solution will beat the AMD platform. However, you are looking at the greatest value at a set price point, it's hard to really knock the AMD platform because of the power you can get at that same price. Not too long ago we set up an HP DL385 G7 as well with dual Opterons and it has more than enough performance and flexibility to meet our needs as we are only needing to run three VMs off of it. But when we bought it it was by far the best option as it gave us far more performance headroom and came initially with more included than going with a server at the same price point with Intel.