For a module/script author to accomplish this you design your makefile properly. To read up on the topic, open the POD for ExtUtils::MakeMaker in your browser. Search the text for #!. It's covered there:
Ref to array of executable files. The files will be copied to the INST_SCRIPT directory. Make realclean will delete them from there again.
If your executables start with something like #!perl or #!/usr/bin/perl MakeMaker will change this to the path of the perl 'Makefile.PL' was invoked with so the programs will be sure to run properly even if perl is not in /usr/bin/perl.