You’ll get the highest quality images out of the D90 if you:
• Shoot NEF format. You have the original sensor data to deal with, and can apply different interpolation routines on it after the fact.
• Get the exposure right. Incorrect exposure has impacts on all kinds of image quality issues, including visibility of noise, contrast, and much more. Any underexposure of a D90 image tends to produce more visible noise, especially if you adjust the exposure later in post- processing. Note that you can check channels individually on the D90, so there’s no excuse for blowing a channel, either. However, to keep from doing so when you’re shooting NEF, you should also set the proper white balance setting (the histograms are calculated from the embedded JPEG, which means that the white balance data is reflected in the histogram!).
• Keep the sensor clean. Even with Photoshop’s Healing Tool or Capture NX’s Dust Off function, you’ll still end up spending some time cleaning up dust bunnies in large bright areas of images shot at small apertures. Plenty of quick and good cleaning options exist now, so use one regularly, such as the Sensor Brush.
• Shoot at the lowest ISO you can, and use Long exp. NR (noise reduction; on the SHOOTING menu) on exposures over 8 seconds. (This form of noise reduction does not lower detail.) Once noise is recorded in an image, getting it out is difficult at best, impossible at worst. ISO 200 is where you want to be as often as possible—at this value the D90’s images are nearly noise free and have a great deal of detail and clarity. If you shoot at high ISO values you have to make a choice: detail or not. Turning on High ISO NR (noise reduction) will cause loss of some detail in JPEG images, though the noise will be better controlled.
• Keep your camera cool - Noise generation increases in the camera as the temperature rises. Bear that in mind.