I'm trying to create a workflow rule or trigger that will only fire when an outbound Email Message was generated by Auto Response rules. Is there a field (or a set of fields) that can be used to determine this? Is there some other way to identify the Email Message as an Auto-Response message?
You can define auto response rule through out-of-box functionality.
Normally for sending an auto response email we use to define a Organization wide email address like firstname.lastname@example.org
Secondly, this auto response email can be found as Task with Email attribute as checked.
So, based on above two you can identity email
From addresses of auto response email