Ajax Effects using Ajax #commands
I found the best solution to this was using ajax_command_invoke() and layering the required ajax effects together.

For example, you won't be able to directly fade in an element, but you can use replace or prepend, etc., then hide the element, then fade it in.

function my_ajax_callback($form, $form_state) {
  $result = array(
    '#type' =&gt; 'ajax',
    '#commands' =&gt; array(
      ajax_command_replace($selector1, $html1), //add your element
      ajax_command_invoke($html1, 'hide'), //hide it
      ajax_command_invoke($html1, 'fadeIn'), //now use the effect you're after
      ajax_command_replace($selector2, $html2), //add your other element
      ajax_command_invoke($html2, 'hide'), //hide it
      ajax_command_invoke($html2, 'show'), //use the other effect
    ),
  );
  return $result;
}