I'm trying to disable a particular system workflow message from being sent out - "Events - Pending Registration Expiration Notice". I've had a look in the event configuration and have found nothing that would indicate being able to disable this message per event. Is there another place that this can be disabled?
Use the hook civicrm_alterMailParams.
Inspect the $params that are passed in, and if you don't want the message sent, set $params['abortMailSend'] to '1' (or any non-empty value).
See lines 71-77 of CRM/Utils/Mail.php to see how this is processed by CiviCRM. This doesn't work for CiviMails but works for other emails sent by CiviCRM.