I agree with the observation (from other peoples tests - I don't have a D3) that the Canon images clean up nicely with some noise reduction and the D3 doesn't, and that after that NR on the Canon images the difference seems less than 2 stops. But really even a 1 stop improvement on the 5D is pretty impressive.
My test images indicate the D3 is definitely not as much as a 1 stop improvement on the 5D in terms of noise at high ISO. What I think is happening here is that many photographers, both amateurs and professionals, are getting bamboozled by the unprecedented high ISO numbers.
An exposure at ISO 6400 is not necessarily one stop less than an exposure at ISO 3200. The ISO numbers are only an indirect and approximate indication of what the actual exposure might be.
For example, a D3 shot at F11 and 1/30th is one stop less than a 5D shot at F8 and 1/30th. I can show you two such shots and several 100% crops. I think you'll agree the D3 shot is clearly noisier.
I mentioned earlier that i thought the D3 noise advantage over the 5D is of the order of 1/4 to 2/3rds of a stop. Having now examined more images from both cameras, I believe it is actually less. More like 1/4 to 1/3 of a stop.
The final image compares the 5D at F8 and 1/50th with the D3 at F11 and 1/30. That's 1/3rd of a stop difference. I still think the 5D has a slight edge here, but there's no point in arguing whether it's really 1/4 stop or 1/3rd. Let's just say it's definitely less than one stop and apparently less than 1/2 a stop.
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I should mention that none of the above images have been resampled. The 5D image is slightly larger because the file size is larger (72.8MB as opposed to 69MB for the D3). There is also a slight discrepancy in focal length due to inaccuracies of the zoom labelling, but only slight. This should not affect noise results to any noticeable extent.