This should work.
Applications -> Automator -> Custom
Use: "Run Shell Script"
Replace the 'cat' with:
PROGRAM=/path/to/your/unix/command/line/program # YOU CUSTOMIZE THIS LINE!!!
SCRIPT=/tmp/Drag-N-Drop-Terminal-Starter.$$
( printf "#!/bin/bash "
printf "${PROGRAM} %q " "$@"
) >"${SCRIPT}"
/bin/chmod +x "${SCRIPT}"
/usr/bin/open -a Terminal "${SCRIPT}"
/bin/rm "${SCRIPT}"
VERY IMPORTANT: Change the "Run Shell Script" -> Pass input to "as arguments". This is a button in the upper right corner of the "Run Shell Script" Automator box. If you forget this step, the "Run Shell Script" will not see your file name.
Automator -> File -> Save As... -> Application
You now have an application with .app that you can associate with your file, or all files with that .type
Select a file you want your /path/to/your/unix/command/line/program to process when you double-click on the file.
Finder -> File -> Get Info
Change "Open with:" -> Other... Find your saved Automator .app and choose it as the application you want to open the file with.
Optionally click "Change All..." but ONLY if you want every file with the same .type to be processed by your program.