Hooking Into Widget Output Loop

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;
}