$params = array(
'product' => $item->getProduct()->getId(),
'related_product' => null,
'options' => array(
1 => 3,
),
'qty' => 3,
);
$cart = Mage::getSingleton('checkout/cart');
$product = new Mage_Catalog_Model_Product();
$product->load($item->getProduct()->getId());
$cart->addProduct($product, $params);
$cart->save();
Mage::getSingleton('checkout/session')->setCartWasUpdated(true);