It depends on which notification handler is used, in the case of the subtree handler you can modify the template design/standard/templates/notification/handler/ezsubtree/view/plain.tpl
If you look in the same directory you will see the file digest_plain.tpl and a digest_element_plain.tpl, they are used when sending out email using digests.
Generally speaking the templates will be in the view subdirectory of the notification handler. All notifications templates are found in design/standard/templates/notification