Hook into 'dynamic_sidebar'
and count how often it is called.
You get the current active sidebar with key( $GLOBALS['wp_registered_sidebars'] )
.
add_action( 'dynamic_sidebar', 'wpse_96681_hr' );
function wpse_96681_hr( $widget )
{
static $counter = 0;
// right sidebar in Twenty Ten. Adjust to your needs.
if ( 'primary-widget-area' !== key( $GLOBALS['wp_registered_sidebars'] ) )
return;
if ( 0 !== $counter && 0 === $counter % 3 )
print '<hr>';
$counter += 1;
}