Do NOT upgrade a Production Website running multiple stores to the new 1.4.0.1 release. It will BREAK your other sites.

Magetnto made important changes to the index.php file in the root directory. If you upgrade a production (live) Magento site that is supporting multiple store view, stores, or websites, the new index file will cause your dependent websites or stores to break. This was reported to me just a short time ago from one of my customers in the UK.