When you display a RAW image on your computer in a program like Nikon Capture or View NX2, you are seeing the image displayed with the settings you used at the time you took the picture. However, since a RAW file is not yet an image, none of the settings are permanently applied until you save it as a JPEG or another format.
Proof of this is how easily you can modify the RAW file with a change of settings in the computer software you are using. If you shot it with Cloudy White Balance, you can change it to Shady White Balance and it will be exactly the same as if you shot it originally in Shady instead of Cloudy. If you used the Neutral Picture Control and decide you'd rather use the Vivid Picture Control, change it in the Nikon software and it will be as if you had shot with Vivid in the first place—after you save the image as a different format. You can even save the RAW file with your new settings, but they are still not applied permanently to the image, they are just saved as new markers for later display in-computer.
Since a RAW file does not become an image until it is saved as another format, you can play with it, modify it, or change it as much as you like, and the final result will be as if you used the new settings when you first took the picture.
One exception to this rule is Long Exposure Noise Reduction. The reason is that, using this method, two exposures are combined in a black frame subtraction, and I've not found a way to remove the second exposures results.
This goes to good exposure methods, one of which is Long Exposure Noise Reduction. It only applies to exposures over 8 seconds long, and you must have Long exp. NR turned on, so most of us will not use it often. I leave it turned on all the time but I rarely take exposures longer than 8 seconds.
For those that wonder about Long Exposure Noise Reduction (Shooting Menu > Long exp. NR), it does not blur the image, after the fact, like normal noise reduction. Instead, it is concerned with pixels that get warm and bright during a long exposure. It takes the first exposure as normal, then it closes the shutter and takes a second exposure of the exact same length (except that the new D7000 claims it can make the entire combined exposure at between 1.5 and 2 times a single exposure's length). After both exposures are complete the camera examines the first and second images (in a sense) and combines them. How? Most of the second exposure is totally black, of course, since the shutter is closed. The camera sees where there are any loud, bright pixels in the second exposure and subtracts them from the first exposure.
So, the first exposure really only gets reconfigured by the second exposures results. This does not damage the image nearly as much as regular noise reduction. However, this method of noise correction is applied to the RAW image in a permanent way. That's because it is part of the exposure itself, and becomes part of the RAW data being passed to the camera card. There is no way, that I know of, to remove the results.
RAW shooters have learned that RAW (NEF) files are completely flexible and changeable after the fact. Do not worry about what settings you have used on a RAW file, you can change it later. The important thing with RAW files is that you get a correct exposure. That's one thing that cannot be changed after the fact without damaging the appearance of the image. Learn to use your histogram to validate the exposure. Make sure you have correct settings for depth of field (aperture) and motion control (shutter speed), then shoot with abandon as to settings. You can change it all later and it will be as if you used the new settings when you took the picture originally.
No RAW file exists as an image until you save it as a JPEG, TIFF, or other format. Things like noise reduction, white balance, Picture Controls, sharpening, and contrast are applied permanently only at the time the RAW file is saved as something besides a RAW file. RAW files stay raw; that's why RAW (NEF) makes such good storage format and so many experienced photographers shoot with it.
Keep on capturing time...