Re: One item that hasn't seemed to have been noted by anyone is that the 3800 X2 used in the Anandtech review has only half the total L2 cache of the Yonah
You're forgetting that the die size for Yonah is only ~90mm^2, which is less than half the size of a 2x1M X2 processor. AMD has to ramp their 2x512K cache dual cores; otherwise they would not be able to meet capacity demands.
Re: For instance when running single threaded apps such as Doom 3, Yonah's shared cache 2MB is running against the 3800 X2's 512KB per single thread--four times the cache on Intel's side is required to get close to AMD in fps.
Maybe as an academic experiment, you can try to create a system with 512KB Yonah CPU and an Athlon X2 that accesses memory from off of a Northbridge (as opposed to the integrated memory controller), and then see how the two perform. But for real world scenarios, you're going to have to accept the fact that Intel can integrate more L2 cache in a smaller area, while AMD chose to integrate their memory controller for higher performance.