To move the [rt.foo.com #1234] to the end of message subject lines, insert this code into your RT_SiteConfig.pm:

 {
 use RT::Action::SendEmail;
 no warnings qw'redefine';

 sub RT::Action::SendEmail::SetSubjectToken {
   my $self = shift;
   my $sub  = $self->TemplateObj->MIMEObj->head->get('Subject');
   my $id   = $self->TicketObj->id;

   my $token_re = $RT::EmailSubjectTagRegex;
   $token_re = qr/\Q$RT::rtname\E/o unless $token_re;
   $sub =~ s/\[$token_re\s+#$id\]//;

   $sub =~ s/(\r\n|\n|\s)/ /gi;
   chomp $sub;
   $sub = substr($sub,0,80);
   $sub =~ s/\s*$//g;
   $self->TemplateObj->MIMEObj->head->replace( Subject => "$sub [$RT::rtname #$id]",
   );
 }
 }

-- JesseVincent