vApp that were created from a vAppTemplate typically have a metadata entry whose key is
vapp.origin.id and whose value is the ID of the vAppTemplate. Note that this is persisted during instantiation, but can be removed by end-users (with proper permissions), so is not in fact guaranteed to be present.
There are some audit events that are raised during vAppTemplate instantiation, but you cannot rely on those (because they cover other types of things happening to those Templates...).