I use Vuescan which I find much more customizable/tweakable than the Nikon software though the quality of scans it delivers is pretty much the same.
I tell Vuescan to use the "B/W negative" setting, output into 16 bit Gray mode, 1450 dpi (which I find is plenty for monitior viewing & web posting), and I save all scans as .TIF files with no compression.
I don't use any of the special filters like Digital ICE, Grain Reduction, Restore Fading, etc. as I find that I get better results editing the images myself in Photoshop after scanning, if I edit them at all - most of the time the results I get straight out of the camera/scanner are good enough to post without any adjustments.
Oh, and I like to manually set the crop area rather than let the software do it for me, since it will often make strange selections leaving portions of the negative unscanned.
I find it is important to select only an area of the negative itself, and not include any of the black border around it since doing so will make the software automatically change the white balance so that the image looks washed out.
I also make a point of setting Scan From Preview to "Always", and setting the preview resolution to 1450. That way the software only scans each negative once, rather than scanning a seperate Preview.