There isn't a way to include custom fields or tags in the template. I haven't used the fling in a while, but I'm pretty sure it includes all the available email fields.
The way we've setup application based alerts is to create a custom group for each application. You can use VM tags for the custom group criteria, so the group automatically includes all VMs with the application's tag. Then we have a notification rule for each application that is scoped to the group's children (VMs) and has the application name in the rule's name/description. The notification rule name and description are both fields you can include in the template. This isn't ideal for a large number of applications since you would need a lot of groups and notification rules, but it's one way you might do it.