Just to make CountZero's good suggestion more obvious, your code should probably look like this:

#!/usr/bin/perl
use strict;
use warnings;

$^I = ".old";

while (<>) {
   if (/^#!/) {
      $_ .= " ## Copyright (C) 2008 me\n";
   }
   print;
}
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The way you had it, the print would only happen on the line where you made the change. This way, every line is printed, whether you changed it or not.