<?php
function test_form() {
  $form['hider'] = array('#type' => 'hidden', '#value' => 3);
  $form['submit'] = array('#type' => 'submit', '#value' => 'Submit');
  return $form;
}

function test_form_submit($form_id, $form_values) {
  drupal_set_message('<pre>'. print_r($form_values, TRUE) .'</pre>');
}

print drupal_get_form('test_form');
?>

<script>
$('#edit-hider').val(5);
</script>