Rapid File Defragmentor Lite is a freeware command line version.
RapidFD_lite [-r] [a] [-l filelist] file1 file2 ...
Parameters:
RapidFD_lite -r "c:\program files\*.exe" "c:\program files\*.dll"
RapidFD_lite -a abc.dat def.dat
RapidFD_lite -l list.txt