Fixed javascript that removes the need of tracking the clicked container

Drupal.behaviors.popups_reference = function(context) {
  $('.popups-reference', context).not('.popups-reference-processed').each(function() {
    //$(this).addClass('popups-reference-processed'); // Don't re-add to processed links.
    $(this).click(function() {
      var rel = $(this).attr('rel'); // Rel attribute of the clicked link is the wrapper id.
      var wrapper = $(this).parent().parent();

      // Unbind namespaced event, so bindings don't pile up every click.
      $(document).unbind('popups_form_success.popups_reference');
      
      // Bind to the popups API custom form_success event.
      $(document).bind('popups_form_success.popups_reference', function(obj, popup) {
        // Info about the new node was placed in a cookie when it was created.
        var nid = popups_reference_get_cookie_value('PopupRefNid');
        var title = decodeURIComponent(popups_reference_get_cookie_value('PopupRefTitle'));

        wrapper.find('select').append('<option value="' + nid + '" >' + title + '</option>').val(nid); // Select
        wrapper.find(':radio[value=' + nid + ']').select(); // Radio buttons
        
        // Get the first empty autocomplete field to fill (http://drupal.org/node/388406).
        $emptyAutos = wrapper.find('input.form-autocomplete').filter(function(i) {
          return !$(this).val();
        });
        if ($emptyAutos.length) {
          $emptyAutos.eq(0).val(title);
        }
        else { // There are no empty fields, use the first one.
          wrapper.find('input.form-autocomplete:first').val(title);
        }
      });
    });
  });
};

The relevant line here is "var wrapper = $(this).parent().parent();"
If the alter function removes the need to add a number to the class selector
popups-reference-0 to popups-reference
The javascript could look like this

"var wrapper = $(this).parent('.popups-reference');"

this way, there is no need to use a id counter after each popups-reference and then solve one problem I had with multigroup module (cck 3.x)

When a cck group is added, it doesn't recall the alter form because it use a cached form. In other words the counter doesn't get incremented or always stays at 0 because multigroup only add a new group at a time.

I also added a line which will add a new option to select field so it can select it.