Students at my workshops have noticed that I apply a wide range of "corrective measures" to NEFs converted by Lightroom and ACR. Now Adobe has fully embraced the "profile it yourself" technique that many of us have been using for years.
As part of an update to the DNG specification, Adobe has produced a beta DNG Profile Editor. Don't let the name fool you. Even though DNG is in the name, profiles you produce with it can be used with ACR 4.5 and Lightroom 2.0 converters as well as the current DNG converter. Note that you need the newest Adobe converters to use this function, however; older versions won't recognize the profiles. If you're going for accurate color, you should also use images of the ColorChecker chart taken at 2850K and 6500K to create your profiles.
Basically, you create a camera profile using the DNG Profile Editor, and that can then be chosen via the Camera Profile pop-up menu in the Camera Calibration tab in the Adobe converters. Adobe provides a great deal of details, tutorials, and more on the Web site referenced above, including how to then set your profile so that it is the default in your converter. Bravo.
Note that there is more to it than that, though. As part of the beta, Adobe has produced "camera matching" profiles for the eight basic Nikon Picture Controls (several are named with the D2X prefix, even though they apply to all the Nikon bodies with Picture Controls; these correspond to the downloadable Picture Controls Nikon has supplied to mimic the D2x [hmm, mimics of mimics]). These camera matching profiles only mimic the default Picture Control settings, though (i.e., they don't account for any in-camera changes you make to your Picture Controls).
The profile editing capability is a nice new addition to the Adobe products, and one that I'm probably going to suggest that all Nikon users take advantage of if they use the Adobe converters. (The "probably" in the last sentence means I haven't yet come to a conclusion about what the best way to get optimal conversions out of the new converters is. But it seems clear already that using the "right" profile is a better starting place than we've been using.) Unfortunately, I just finished updating my Introduction to Nikon Software book to version 2.0, so any elaborate suggestions I have on this will have to wait until the next revision.