The best software for handling NEFs in terms of out and out quality is Capture NX2. Nothing else comes close for getting the white balance and colours bang on and giving you the shot you saw through the viewfinder in my experience. However it only works with NEFs, TIFFs and JPEGs, so if in a years time you sell the Nikon and get a Sony or you plan on importing files from another brand of camera you'll need new software to get the best out of it, which is a bit limiting.
Lightroom is very convenient and flexible allowing you to import, catalogue, edit and export photos from one place. It doesn't render NEFs particularly well though, reds go orangey, highlights get blown, it can posterise some areas…
Apple's Aperture does a slightly better job with NEFs, still not as good as Capture but more convenient, if you don't have a Mac then obviously it's no good!
