I've been publishing my results in the Nikon SLR forum at DPReview for a while now, but I hadn't registered as a Nikonian until today. However, I've been wanting to share with you my findings.
After noticing "underexposure" in my photographs with the D100, I decided to do several tests. I wanted to find out if the camera was indeed underexposing. So I tested my D100's meter against my faithful Nikon FA's meter which has always given me near-perfect exposures. I found that both camera's metered the same. Then I photographed evenly lit walls with the default tone settings on my D100 and found that the histograms were centered at a point midway between the lower quarter and the midpoint of the histogram range. After taking 30 photos with the same results, I concluded the tone curve was off.
I then experimented and created 3 tone curves with resulting histograms that matched almost exactly the histograms created when setting +0.3, +0.5, and +0.7 EV corrections with the normal tone curve setting. The tone curves curves were further tested thoroughly to ensure they did not introduce any color changes or blow out highlights any more than the default tone setting.
You can download my custom tone curves here (recommend using +0.5 ev equivalent curve for general use): http://fotogenetic.fade.to
Try them out if you are unsatisfied with the default tone settings. They've worked well for me.