Let's say you disabled Mage_Dataflow but enabled Mage_Catalog and the system is presenting you:
"Mage_Catalog" requires module "Mage_Dataflow"
You have two possibilities:
Mage::run()
Mage::run($mageRunCode, $mageRunType, array(
'config_model' => 'Zookal_Mock_Model_Config'
));
The config model Zookal_Mock_Model_Config
will automatically resolve invalid dependencies for disabled modules. But some dependency really make sense ;-)