I've noticed that at ISO 100 the Nikon D3X does much, much better in the deep shadow areas than the Canon 5D Mark II. However, it doesn't do much better in the midtones or highlights.
If we look at DXOMark's tests, we can see that with the Signal-to-Noise @ 18% grey chart, the cameras have almost identical levels of noise. This should indicate that the noise levels are the same, but it does not. We have to look at the full SNR graphs in order to get a fuller picture.
Let us say that we require for "acceptability" a Signal-to-Noise ratio of 18 dB. Looking at the full SNR graphs on DXOMark, the Nikon D3X achieves this signal strength at about 0.25% on a logarithmic scale. The Canon 5D Mark II achieves this signal strength at about 0.66% on a logarithmic scale. This implies that we can push the shadows from the D3X over a stop before they have the same noise level as the 5D Mark II. Essentially, for the deep shadows we can shoot a stop underexposed and push in post to achieve similar quality.
This would be why the D3X is rated as having 13.65 stops of dynamic range at ISO 100 while the 5D Mark II is rated as having only 11.86 stops of dynamic range.
One last thing is that this does not take into account that the 5D Mark II has significantly more pattern noise in the shadows. This makes it much more noticeable.
In essence, I really hope that we see more cameras producing deep shadow noise similar to the D3X in the future.