That's it guys! Adding the print statement and the newline is what did it! You guys rule! And I just know if I persist at learning this stuff, obvious things like this won't bite me in the ass anymore.

Cheers!

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

$^I = ".bak";
while (<>) {
  if (/^#!/) {
  $_ .= "## Copyright (C) 2008 by C'est Mois\n";
  }
  print;
}
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