Now we finally have a somewhat scientific side-by-side comparison of the raw files from both bodies, courtesy of Imaging Resource.
To make this comparo as precise as possible, I thought it made sense to compare the Nikons NEF files with no noise reduction applied to the Canon's CR2 files. Truthfully, I had a very hard time distinguishing the the 5DIII images from the D800 images. The noise, DR, and overall IQ are just so freakin' close. Maybe the 5DIII starts to edge ahead after ISO 3200, but it is the slightest of advantages. I tried to compare them at 51,200 and 102,400 as well, but IR must have forgotten to test the D800 at those ISO speeds
DR wise, there is a noticeable advantage in the Nikon's shadow details, but again, it's only the slightest of advantages. Call me crazy, but I actually think the extra DR makes the Nikon's files look flatter. I also prefer the 5DIII's color reproduction, and the files look a tad sharper granted that might be attributable to the lenses. On a purely subjective level, to me the 5DIII's files just look better, but again, under identical shooting situations the two cameras produce nearly identical images.
After pixel peeping for about an hour, it really put into perspective what terrific tools each of these bodies are for creating fantastic art. It also put into perspective how silly it is to argue about the pros and cons of each body when it requires an hour of pixel peeping to attempt to distinguish any differences in IQ between them.
That's just my worthless opinion. Discuss