There is no question the Nikon D800/E is a spectacular camera. But
just how well does the D800 stack-up against the venerable Nikon D3s?
What about in DX crop mode; how well does it fare against the D7000? We
now know the new Nikon D800 has a bad case of multiple personality
disorder. The D800 is several different cameras, rolled-up into one very
sleek and attractive body.
Let's examine just how well the D800 performs when down-sampled to
12.1 megapixels to match the un-defeated high-ISO king, the Nikon D3s.
In addition to this comparison, we're also going to put the Nikon D800
against the current APS-C DX crop champion, the Nikon D7000.
Nikon D800 vs. Nikon D3s
The D800/E is capable of achieving amazing amounts of detail at its
native resolution of 36.3 million pixels. This is great for studio and
landscape work or anything that warrants this kind of resolution.
However, the final output doesn't always need to be the native
resolution of 36.3 MP. What we've found is the D800 has excellent
Dynamic Range combined with excellent high-ISO noise characteristics,
giving us the ability to down-sample when need-be, while retaining all
of the high-frequency detail captured by the high-resolution sensor. We
know that down-sampling an image helps to reduce noise (especially
luminance noise), so we reap the benefits of lower noise
and
better detail, while retaining the D800's excellent Dynamic Range (DR)
when down-sampling. A down-sampled image that has more high-frequency
detail is a better candidate for noise-reduction via software (Lightroom
4, Topaz DeNoise...etc) and can handle more aggressive noise reduction,
while still retaining high-frequency detail that's usually lost
during aggressive noise-reduction.
For this comparison, we shot both cameras at the same respective
exposure, ISO, aperture and white balance and set both cameras to the
"STANDARD" Picture Control with no additional capture sharpening,
contrast, brightness, saturation or hue. Both cameras were shot in
RAW(NEF) format and developed into a high-quality 8 bit JPEG format
using Capture NX2 with zero High-ISO Noise Reduction. The D800 shots
were then opened in Photoshop and down-sampled using Photoshop's
"Bicubic Sharper" algorithm to 4256 x 2840 px to match the D3s'
native resolution. No other sharpening was performed
(click on any image to enlarge it).

D3s vs D800 12mp ISO1600 Crop 1

D3s vs D800 12mp ISO3200 Crop 1

D3s vs D800 12mp ISO6400 Crop 1

D3s vs D800 12mp ISO12800 Crop 1

D3s vs D800 12mp ISO25600 Crop 1
As you can clearly discern, the D800 image retains much more
high-frequency detail throughout the ISO range. The D3s does beat the
D800 in luminance noise by about a third-stop, with chrominance noise
being significantly worse in the D800's files above ISO-12800. As stated
above, the D800's file can handle much more aggressive noise reduction,
while retaining much of its detail, which will result in a better
overall file than the D3s until about ISO-25,600. At this point, the
D800's files are riddled with amp noise which is destroying most of the
high-frequency detail advantage it had over the D3s, making the D3s a
better option from ISO-25,600 and up (The only way the D800 can go above
ISO-25600 is by "pushing" in post).
While the D800's DR is supremely impressive at base ISO (ISO-100) to
about ISO-800 (about 14.3EV @ ISO-100), it falls off at higher ISOs.
This is where the D3s shines; the D3s has less DR fall-off at upper
ISOs, but several stops less DR at base ISO as compared to the D800.
While the D800 doesn't quite beat the D3s in high-ISO noise handling
when down-sampled to 12.1 MP (without noise reduction), the D800 will
clearly out-perform the D3/D700 sensor in noise, sharpness, detail and
DR, at every ISO, when down-sampled to the same resolution of 12.1 MP.
Let's look at a different set of D800 vs. D3s crops, this time
focusing on the high-frequency detail in the books on the bottom shelf.

D3s vs D800 12mp ISO1600 Crop 2

D3s vs D800 12mp ISO3200 Crop 2

D3s vs D800 12mp ISO6400 Crop 2

D3s vs D800 12mp ISO12800 Crop 2

D3s vs D800 12mp ISO25600 Crop 2
Once again, you can clearly see the high-frequency detail advantage
the D800 has over the D3s, when down-sampled to 12.1 million pixels.
Look at the dark brown book on the left side of each crop; the D800
clearly renders the detailed fabric cross-hatching @ ISO-12800 and can
just barely be seen @ ISO-25600. The D800 files are sharper and retain
more high-frequency details at every ISO.
Nikon D800 vs. Nikon D7000
While the D800/E is 36.3 MP in FX mode, the D800/E has a DX (1.5x
crop) mode, which is 15.4 MP. The Nikon D7000 is a 16.2 MP APS-C DX
format camera that currently sits atop the APS-C camera heap, having the
best performing APS-C sensor in the world, based on the Sony Exmor 16.2
MP sensor (this 16.2 Sony Exmor sensor is used in several other cameras
on the market). Since the D800 has a DX crop mode that's roughly the
same resolution as the D7000's sensor, we wanted to see how the D800
performed in comparison to the D7000. Please keep in-mind, the D7000
does have a slightly higher resolution, although not by much.
The D800 has a pixel pitch of 4.88µm, while the D7000 has a pixel pitch of 4.78µm, the .10µm is
almost insignificant, which means the pixel pitch is
roughly
the same in both cameras, with the D800 having a slightly larger pixel
pitch. This also helps us come to the conclusion that the D800/E sensor
is based on a Sony Exmor design, although this is still yet to be
confirmed, but is widely rumored to be true.
As with the D800 vs. D3s comparison, we shot both cameras at the same
respective exposure, ISO, aperture and white balance and set both
cameras to the "STANDARD" Picture Control with no additional capture
sharpening, contrast, brightness, saturation or hue. Both cameras were
shot in RAW(NEF) format and developed into a high-quality 8 bit JPEG
format using Capture NX2 with zero High-ISO Noise Reduction. No other
sharpening or post-production was performed.
Let's examine the D800 vs. D7000 image comparisons
(click on any image to enlarge it):

D800 vs D7K ISO1600 Crop

D800 vs D7K ISO3200 Crop

D800 vs D7K ISO6400 Crop

D800 vs D7K ISO12800 Crop

D800 vs D7K ISO25600 Crop
As you can see, the D800 does out-perform the D7000 at every ISO,
although in luminance noise, they are closer at lower ISOs. Where the
D800 shines is sharpness, micro-contrast and chrominance noise. Even
with the D7000 having slightly better resolution, the D800 has much
better effective resolution, which shows as a sharper image and better
high-frequency detail. Not only does the D800 out-perform the D7000 in
detail, micro-contrast and luminance noise, the D800
has significantly less chrominance noise. This is exaggerated as the ISO
rises. An example of this can be seen below.
The D800's sharper image and more high-frequency detail might point
to a weaker OLPF (Optical Low-Pass Filter a.k.a. AA-Filter) on the D800.
The D800E would reveal even more sharpness, micro-contrast and
high-frequency detail as compared to the D7000, due to its
Anti-Aliasing characteristics being canceled-out in the D800E's OLPF
filter stack.
Example of D800 vs. D7000 chrominance noise at ISO-25600:

Nikon D800 vs. D7000 ISO-25600
I've made the full-resolution images available at the bottom of
this article, I highly suggest the images to be downloaded and compared
full-size, for full-effect. Looking especially at the more finely
detailed writing on the book ends.