When working in low light, shoot in RAW and err on the side of overexposure.
If you have to shoot using high ISOs, the best way to prevent noise from building up in the shadow areas of your image is to make sure not to underexpose. If you shoot in RAW, you will be able to recover mild blown highlights (but don’t go crazy — there are limits to what you can get back with RAW) quite cleanly, but if you try to recover detail from the shadow areas, noise will eat your lunch.
If you’re using Capure NX 2, the easiest way to recover the highlights is to use “highlight protection” in the quick fix menu. In NX 1.x, you can reduce the exposure compensation, then tweak the levels and curves to make sure you don’t bring down the midtones.
Turn off in-camera sharpening and noise reduction
In-camera sharpening is not very intelligent. Either turn it off in-camera, or else turn it off in Capture NX before you begin editing. In-camera noise reduction is both dumb and slow, so definitely turn that off in-camera.
Think locally, act locally,
Sharpening and noise reduction are not mutually exclusive, but they’re close. When you reduce noise, you reduce sharpness. When you sharpen an image, you sharpen the noise. You can ameliorate this somewhat by tweaking the settings — increasing the “sharpness” slider in noise reduction, and careful application of high pass sharpening (and avoiding unsharp mask if possible) will both make it easier for you to have both sharpness and noise reduction in the same area.
But it’s not likely that you need every inch of your image to be sharp, and it’s not likely that every inch of the image needs the same degree of noise reduction. So, apply both your sharpening and your noise reduction locally, where each is needed most. This is easier in Capture NX 2, because selection control points allow you to work quickly to isolate the areas you need to effect. Just drop selection points at full opacity in the areas you want sharp and partially or totally reduced points where the image is supposed to be soft. Similarly for noise reduction.
Of course, sometimes you’re going to have a lot of noise in areas you need sharp — it can’t always be avoided.
If you don’t have NX 2 yet, you can perform the same localization by masking the areas in question manually. This will be much, much, much easier if you have a Wacom tablet. It gets tedious very quickly is you use a mouse.
Intensify the highlights and shadows
If your image contains dark shadow area where detail is going to be lost anyway, or where the detail is really noisy, consider using control points or an LCH adjustment to shove those areas closer to pure black. Also brighten the lighter areas where noise should be at its minimum already.
Convert to black and white
Noise looks better in black and white. use the BW conversion menu, play with the filter settings, find what works best for your image.
Convert to black and white, even in color
Bear with me. Even if you’re going to want a color image as your finished output, you may want to make a trip to the BW conversion menu. Try converting to black and white and playing with the opacity settings. Often a conversion with partial screen or multiply opacity can help emphasize the areas of an image you want sharp, especially if you figure out what color filter setting to use.
Convert to black and white, again
I’ve found that in some situatuions, it’s helpful to do a blue-filtered BW conversion applied with partial screen opacity, followed by a second black and white conversion applied normally or as an overlay, with green filter setting. Sometimes this helps brighten and clarify an image without increasing noise.
Not sure exactly under what conditions this works best; I’m still experimenting.
Desturate the noise
Here’s another area where Capture NX really shines. If you’re going to keep the image in color, one way to make noise more pleasing without actually having to reduce it is to drop a control point into some of the noisy areas, crank the saturation to 0, and then drop control points into areas that are relatively noise-free but otherwise similarly colored. The effect will be overall reduced saturation and a possible change in color balance, but if done correctly, it also renders the noise less noticeable and more like film grain.