No 'make'. In my backup, I found that I had /usr/bin/make as a link to gnumake. I guessed that was installed by Xcode, so I reinstalled Xcode from its .dmg. I could have simply rsync'd /usr/bin from backup, but I do recall having to explicitly reinstall Xcode even after copying everything in '/' (see §5.6). After that, I did an rsync -aunv (note the 'n' meaning ``dry run'' or ``not really'') to see if anything else might be needed for /bin, and only /bin/launchctl was listed. (I left it alone.)
I also later learned I had to install iTunes from the .dmg. It must leave some cookies in the system somewhere that it insists on finding--rather odd for a free app.
I also later found out Logic was ``zombified''. Maybe I'll reinstall it some day.
My EPSON Scan.app utility just dies when you try to launch it. Reinstallation from epson12645.dmg fixed it. Must be installing stuff in system directories.
Ok, some MacPorts needed to be reinstalled (port uninstall foo; port install foo) as well (not sure this was related): maxima, sox.
I also needed to copy /Library/Application Support/Adobe/ (half a gigabyte of stuff!). Otherwise, I ran into missing fonts, and Distiller would not even launch. I guess /Library is not a system folder since it includes files installed by apps installed by users.