Testing your code, my testfiles were altered. I had a .bak file containing the old content and the "original" file was empty.

You lack a print statement in you while loop to print the file contents.

#!/usr/bin/perl -w
use strict;

$^I = ".bak";
while (<>) {
  if (/^#!/) {
  # BE AWARE OF THE NEWLINE
  $_ .= "## Copyright (C) 2008 by C'est Mois\n";
  }
  # BEWARE THIS: prints $_ 
  print;
}
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