item_options.php

<?php

require_once 'app/Mage.php';
Mage::app();

$quote = Mage::getModel('sales/quote')->load(197643);
/** @var Mage_Sales_Model_Quote_Item $item */
foreach ($quote->getAllVisibleItems() as $item) {
    $option = $item->getOptionByCode('additional_options');
    $additonalOptions = array();
    if ($option) {
        $additonalOptions = unserialize($option->getValue());
        foreach ($additonalOptions as $key => $additonalOption) {
            if ('my_code' === $additonalOption['code']) {
                unset($additonalOptions[$key]);
            }
        }
    }
    $additonalOptions[] = array(
        'code'  => 'my_code',
        'label' => 'This text is displayed through additional options',
        'value' => 'ID is ' . $item->getProductId() . ' and SKU is ' . $item->getSku()
    );
    // @see Mage_Catalog_Helper_Product_Configuration
    // @see Mage_Catalog_Model_Product_Option_Type_File
    $item->addOption(new Varien_Object(array(
        'product' => $item->getProduct(),
        'code' => 'additional_options',
        'value' => serialize($additonalOptions),
    )));
}
$quote->collectTotals();
$quote->save();