Best way to do this is using Magento collections.
Create a new PHP file, include Mage.php
, initialize the application and make your changes.
It might take a while depending on product count.
I think you want to do something like that:
require_once('../app/Mage.php');
Mage::init();
$product = Mage::getModel('catalog/product')->getCollection()->addAttributeToSelect('*');
$store_id = 1;
foreach ($product as $prod)
{
if ($prod->getCategoryIds() == NULL)
{
Mage::getModel('catalog/product_status')
->updateProductStatus($prod->getId(), $store_id, Mage_Catalog_Model_Product_Status::STATUS_DISABLED);
}
}