Basic data setup script for migrating config settings using store code.

data-setup-config-migrate.php

/* @var $installer Mage_Core_Model_Resource_Setup */
/* @var $storeObj  Mage_Core_Model_Store */
$installer = Mage::getResourceModel('core/setup','core_setup');

foreach (Mage::app()->getStores(false,true) as $storeCode => $storeObj) {

    switch($storeCode){

        case 'somecode':
            $path  = 'design/theme/default'; //or one of design/theme/{layout|locale|skin|template}
            $value = 'theme_name';
            break;

        case 'anothercode':
            $path  = 'design/theme/default';
            $value = 'another_theme_name';
            break;

        //...
    }

    //write to DB
    $installer->setConfigData(
        $path,
        $value,
        'stores',
        $storeObj->getId()
    );

    //Log query
    Mage::log(
        $storeCode.': '.$value,
        Zend_Log::INFO,
        'theme-setup.log',
        true
    );
}