Using GNU parallel: http://www.gnu.org/software/parallel/
GNU parallel
I have a program that takes two arguments, e.g.
$ ./prog file1 file2 $ ./prog file
You are probably looking for --colsep.
--colsep
generate_file_pairs | parallel --colsep ' ' ./prog {1} {2}
Read man parallel for more. And watch the intro video if you have not already done so http://www.youtube.com/watch?v=OpaiGYxkSuQ
man parallel