I went to a D200 class and the instructor was talking about Nikon Capture. He said that you could save ORIGINALS as NEFs. This includes JPEGs, if you shoot JPEG instead of RAW. There can be advantages for saving original JPEGs out of NC which I won't go in to.
Rich,
I have something to say about this and you won't like it: NEF is a proprietary format owned by Nikon (same for PSD files being owned by Adobe).
This is even more painfully obvious with Capture NX where a NEF has additional PATENTED U Point (TM) (by Nik Software) instructions embedded within the NEF.
Of course, none of this information is documented (one of those obnoxious consequences of being proprietary), and any type of support for these formats would have to be from reverse engineering which is not only very difficult but of questionable legality, especially when it is patented or if the data is encrypted in any way (DMCA) - not that Nikon would do such a thing. The only hope is to look for the original image data (whether it be RAW, JPEG, or color TIFF) and be able to display that, or perhaps a proxy thumbnail/preview.
I will try to make Photo Mechanic be able to view the original JPEG stored within a NEF, but any adjustments you make in Capture (NX) will not show until you use Capture to save a non-proprietary version. The same limitation is true for any other software other than Nikon's unless Nikon updates the embedded thumbnail or preview proxy, or provides software developers with a useable SDK that can render these embedded "non-destructive" instructions.
In the meantime, I hope you are keeping the original JPEG or NEF files in addition to the new ones saved by Capture (NX) for the advantages that you didn't mention.
BTW - Nikon could have chosen to embed their proprietary instructions within a JPEG or TIFF file such that the original image data would be readable in a standard fashion by any standard type of software, but instead they chose to embed your JPEG or TIFF file inside of their proprietary format along with their proprietary and patented instructions.
--dennis