I've had the D800 for a while now and have had the chance to shoot with it in less than ideal lighting - mostly between 6 and 7am when bird activity is at it's highest. One thing that has constantly surprised me is the great high ISO capability of this camera as I bought it resigning myself to dealing with significant noise. After a couple of months of shooting, I find myself comfortably shooting into the ISO 3,200 range when the light calls for it, and switching to my D3S only beyond that. The next question to me was - how does it compare against the venerable D3S that was until recently (and some say still) the king of low light / high ISO shooting?
My test included shooting both cameras in controlled lighting (the light from a single incandescent bulb) and set up on a tripod. All images were taken with the Nikon 16-35mm f/4 lens with VR switched off. The pictures were shot in RAW, viewed side by side in Adobe Lightroom 4 at 1:1 ratio (hence the much larger images from the D800), and a screen capture was taken. 
Please note that this test is ONLY intended to show noise and not resolution - from looking at the samples I can see that the D800 was out-resolving the printing capabilities of this seed manufacturer (the subject is a packet of seeds)!

Here are the results of my testing:

ISO 100-400 The images look pretty much the same, save the D800 delivering demonstrably more resolution with a hint more noise. 

D800 ISO 400


D3S ISO 400

ISO 800 I can see a little luminance noise in the D800 image, but nothing that would bother me. The D3S file looks clean.

D800 ISO 800


D3S ISO 800

ISO 1600 A little more luminance noise in the D800, but still very well controlled and perfectly acceptable, even for very large prints. The D3S is showing some noise, but it's so minute that you need to stick your face in the monitor to see it!

D800 ISO 1,600


D3S ISO 1,600

ISO 3200 The D3S is just warming up, while the D800 is noisier. The noise though is limited to luminance and isn't that hard to get rid of in post processing. On the D800, this ISO is about as high as I would comfortably go for wildlife photography.

D800 ISO 3,200


D3S ISO 3,200

ISO 6400 The D800 gets noisier and some of the fine detail is being blurred at this point. The D3S is humming a tune and picking its nails while still taking incredible pictures in near darkness. Now that's style!

D800 ISO 6,400


D3S ISO 6,400

ISO 12800 The D800 is breathing hard now, with lots of noise, loss of dynamic range and loss of more fine detail. The D3S on the other hand just realized that it's actually in a comparison test! It shows some noise but nothing that can't be cleaned up in post.

D800 ISO 12,800


D3S ISO 12,800

ISO 25600 The D800 is well out of its depth by 25,600 ISO - it's noisy, fine details are all but gone and colors, contrast and dynamic range are suffering visibly. It looks rather like a poorly executed Pointilist painting! The D3S is showing significant luminance noise, precluding this sensitivity for any critical work that'll be printed at large sizes.


D800 ISO 25,600


D3S ISO 25,600

Summary The D800 is perfectly usable for wildlife photography up to ISO 3,200. WHAT? ISO 3200? YES. It's that good! Incredible performance from a camera that many people say is only for use on tripods in controlled lighting circumstances. The D3S maintains fantastic quality right up a little over ISO 6,400, but I'd stop short of using 12,800 for critical work. As the ISO's climb over 3,200, I'd say the D3S is a 1-1.5 stops better than the D800. What was surprising about both cameras was that most of the noise was luminance noise, which to me is not as objectionable as the considerably more difficult to remove chroma noise (those ugly red, blue and green splotches).
This whole test has been based on a pixel level noise comparison, but we're ignoring one key factor here - the D800 has THREE times as many pixels as the D3S!!! To conduct an apples to apples comparison, I resized the D800 image to 12MP, and applied some sharpening and noise reduction to both images. Take a look at the results:

D800 ISO 12,800 - noise reduction & sharpening applied via Lightroom 4


D3S ISO 12,800 - noise reduction & sharpening applied via Lightroom 4

Can you tell a difference? I certainly think they're pretty comparable in terms of noise. So what I see is that the D800 has identical ISO performance to the D3S at ISO 12,800 IF you're willing to spend 15 seconds in Lightroom dragging the noise slider! On top of that, even downsized to 12MP you can see that the D800 is resolving a little more detail. Amazing!

Overall recommendation (based purely on ISO performance) If you shoot a LOT of images in low light and don't want to spend hours in post processing, the D3S is the clear winner here. However, if you shoot in both good and bad light and don't mind spending a little time working on your low light images, the sheer flexibility of the D800 will serve you better. I hope this review has been useful to you, and please feel free to leave comments or ask questions.