If one or all of the following modules (until now) are disabled they will then break the rest of the core:
The Mage_Payment module itself cannot be disabled and mocked because it is too tight couple with Mage_Sales and Mage_Checkout.
Also we can't delete the database tables from some disabled modules as e.g. CatalogIndex relies von customer_group tables or Customer relies on some tax tables when tax is disabled.
At Zookal we have the following modules disabled: Mage_AdminNotification, Mage_Authorizenet, Mage_Backup, Mage_Captcha, Mage_Compiler, Mage_Connect, Mage_GoogleCheckout, Mage_GoogleBase, Mage_Install, Mage_Log, Mage_Paypal, Mage_PaypalUk, Mage_Poll, Mage_ProductAlert, Mage_Review, Mage_Rating, Mage_Rss, Mage_Sendfriend, Mage_Tag, Mage_Usa, Mage_Wishlist, Mage_XmlConnect, Phoenix_Moneybookers.