What happens with the extended Ranges Lo1 (ISO 100 or 50), and Hi1 (ISO 12800) Hi2 (ISO 25600) is that the exposures are shot at normal exposures than pushed the stops.
For Example,
On the D700, Lo1 acts as "ISO 100". What it does is expose an ISO 200 shot for twice as long, than the camera darkens the exposure by a stop. That way you get equal brightness, at twice the length of the expsoure and a drop in noise becuase what little amplification is there is getting pushed down. However, you loose highlight latitude because it was overexposed to start with.
So Hi 1 is just ISO 6400 exposed for half the time, than brightened up.
Hi 2 is 6400 for a quarter of the time and brightened two stops.
it's a pretty simple concept.
Generally, if I can shoot at Lo1, I will. But if my highlights are clipping bad, i'll go to ISO 200 to get an extra stop in the highlights and deal with the noise.
Another thing you can do to escape noise is to stack exposures. Nikons are the only cameras i know of that can do this in camera, but when it works, it makes ISO 3200 look almost like ISO 200. You turn on "multiple exposure", put auto gain on so the image doesn't get too bright, set to 10 shots, and rack off 10 shots of your subject. The camera then puts the pictures together, adjust brightness and bam! clean images. Granted, you have to be on a tripod, but yeah.
What it does is since noise is random, over the 10 shots, the noise is averaged out, so you don't see as much of it, and what's great is that you loose zero detail, and zero dynamic range. A shot at ISO 100 or 200 with this yields so little noise, you can basically sharpen with reckless abandon and you won't pull up any noise.