Are you using Panther (MacOS X 10.3.x)? Do your files still have the file name extension .NEF? Had they by any chance been copied to a Windows server?
I've had a situation at work recently where Quark 4 files, Type 1 printer fonts and a couple of other kinds of files residing on a Windows server were showing up in the Panther Finder as Unix Executable files. None of these files had file name extensions or File type or File Creator tags -- apparently their resource forks had been stripped away. I was able to get them back to normal by adding file name extensions and rebinding them to their proper applications and formats using the utility XRay. No data was lost. Doing a "Get Info" and choosing "Open With" was not sufficient to get them to function in their proper way. Another file attributes utility (freeware) that can do whay I did in XRay is QuickChange (downloadable at Versiontracker).
There are a few other stray reports of the Unix Executable phenomenon reported in Apple's Panther User Discussions--I believe this is always Panther, not any previous version of Mac OS X.