I use Capture NX2 for all my NEF editing. I like the way it takes advantage of my in camera settings. CNX2 is a non destructive editor, the raw data is never changed and the edit steps are saved within the NEF. That means there is only one file to keep track of for each image.
The only time I go beyond CNX2 is for HDR of doing things like perspective correction. For HDR I use Oloneo PhotoEngine and the occasional everything else I use PhotoShop Elements 11.
For browsing, rating, and generation of small JPGs for Web or 4x6" prints I use PhotoMechanic. PhotoMechanic can extract the JPGs directly from the embedded JPG of the NEF. There is no need to even go into CNX2 for that. CNX2 updates the embedded JPG when it saves an edited NEF file.
Gary in SE Michigan, USA. Co-organizer of the Southern Michigan Chapter Nikonians membership - My most important photographic investment, after the camera. D4, D810, D300, D90, F6, FM3a (black), FM2n (chrome) YashicaMat 124, Graflex Speed Graphic 4x5 My Nikonians Gallery & Our Chapter Gallery