For all tests, I used the same exposure for both cameras under the same light conditions with the same Zeiss lens. I wanted to make sure that I captured RAW images in exactly the same settings. Afterwards, I used Lightroom 4.1 (with the latest Adobe profile) and kept color noise reduction and sharpness at 25 percent which are essentially the default values.
Let's examine these 2 areas for shadow detail recovery and compare how much each camera is able to retrieve detail under high contrast lighting.
We begin by taking a look at the image with no recovery and no post-processing.
Canon 5D Mark III
Although the Canon 5D Mark III deals with banding slightly better than the previous version, surprisingly I could still see a substantial amount of color noise.
Nikon D800
Obviously, the Nikon D800 is in a totally different league. Absent of color noise or any pattern, this image reveals Nikon's exceptional performance.
Notice the lower area of the image with no recovery and no post-processing.
Canon 5D Mark III
The Mark III image shows a huge chunk of color noise. Vertical patterns are also visible.
Nikon D800
There is no question that the D800 does not disappoint in signal to noise ratio (SNR) at low ISO and has higher dynamic range. I'm still shocked by the differences.
I know this is disappointing for Canon shooters but on the bright side, there is a workaround if you shoot RAW. Start by overexposing (up to 1 stop) above the correct exposure before taking your shot and then normalize the exposure later in software. This gives you the correct exposure but the shadow detail is much cleaner, just in case you need to push it a stop or two. Alternatively you could use ISO L (50) for low contrast situations whenever lighting and wind conditions allow. However, make sure that there is no clipping in the highlights (blinkies) because essentially when you are using ISO 50, you are already compromising highlight detail by about one stop. I've used this workaround for many years and have been happy with the results.
In regards to the Nikon D800 handing of noise in the shadow areas, I have to say it's nothing short of amazing! Kudos to Sony and Nikon for the new sensor partnership. The Exmor sensor is exceptional and there is so much detail in the shadows. I can push the shadows more than 4 stops without any hint of color noise. WOW! Let's just say the D800 sensor is a breakthrough in sensor technology.
In order to get the most out of Nikon's 36MP sensor, we need to use the best glass at their sweet spot apertures. Apertures too wide will lessen resolution due to lens aberration and too small will rob resolution due to diffraction.

Part III: Diffraction, Anti-aliasing and Conclusion