I own a 5d Mkii, 2 x Mkiii and both the D800 & D800E... I prefer using the 5D mkiii's in most situations. I use the D800/E for product photography as well as some other studio work. I will sell the 5D mkii s as the mkiii are much more responsive, a bit better standard iSO image quality (and much better higher iso performance) and gives me a better success rates at capturing the correct focus, its a much faster responsive camera. The quality of the D800 is excellent especially if you use good technique and are very careful with lens/camera settings, the quality of the images from the 5D mkiii is also excellent but with little, if any care/setup required. The build quality/weather sealing is far better than the D800 and I prefer the default colour balance from the Canon's. The high ISO performance on the Canon is fantastic up to 12800 (above that there is too much noise for me).
Photography outside a studio is often about being quick and capturing the shot, you can't always stage it. So each camera has its use, yes the D800 has 36+ MP and great dynamic range at low ISO especially in shadows/black area but the sensor on the 5D is excellent as well and DXO's markings do not reflect the true "picture".
The programs used for conversion from raw has a dramatic impact on the overall quality of the image including noise.
LR, Aperture, Camera Raw 7.1 (I think it may use the same engine as LR), Phocus, DXO, ViewNX 2, Canon DPP. I would suggest comparing the difference and finding what suits you.