How do I disable a particular notification email, for example the welcome email when a user creates an account?
There is no buit-in ability to disable particular email notifications in Magento. I suggest you to look at the Mage_Core_Model_Email_Template::sendTransactional method. You can overload this class and add check against allowed/disallowed email notifications (based on template name).
Update: you can use extension for disabling specific email notifications in Magento 1.
Also, there is Disable Emails extension for Magento 2.
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