Dave Girard with a shell script for OS X and Linux that collects Nuke files. This latest version makes a relinked duplicate of your scene. Get and use the script from here!
Relinked Nuke Collect script in action from Dave Girard on Vimeo.
“Perfect for archiving your work and even has a check to make sure you wouldn’t accidentally clobber your collected files by copying files with duplicate names. Sorry, I can’t make a Windows version since this is just passing the Nuke file through a lot of UNIX filters like sed, it’s not a binary.”