First, why do a substitution on the body string, it is unnecessary, a match is all you need.

To use that javascript example you'd need to support URL's in the subject. So all in all I'd imagine you'd want to support a single URL in the subject (and use the body for annotation?), or one+ URL in the body (you currently support):

Untested

my $URL = qr/(http:\/\/[^\s]*)/;
#Since we use the expression twice it's nice to have it
#as a variable.
#[TheDamian]'s [cpan://Regexp::Common] would be useful once it
#supplies URL matching
#Until then you might want to expand this, it doesn't
#support port numbers or FTP.


for (my $i=1; $i <= $pop->Count(); $i++) # Loop through messages
{
    #Support personal toolbar button for spontaneity linking
    foreach( $pop->Head($i) ) {
    #If you wanted to get fancy you could use Head in scalar
    #context with multi-line regexp and avoid the foreach
      if( /^Subject:\s+$RE/i ){;
          push @linkList, $1;
      print "$1\n";
          #fetch body for description here if you want
          next;
      }
    }
    my $body = $pop->Body($i);
    #Just a match ma'am
    while ($body =~ /$RE/)
    {
       push @linkList, $1;
       print "$1\n";
    }

    $pop->Delete($i);
 }
 $pop->Close();
[download]

--
perl -p -e "s/(?:\w);([st])/'\$1/mg"