One of the good HMVC examples is the Drupal module system where an add-on module can be an almost standalone application. In Drupal 7, a large module, like the ecommerce module, can have it's own add-on modules to create a three level hierarchy.
Some Drupal themes are HMVC in that they provide administration pages to let the site administrator configure the theme. The theme becomes a subsystem instead of just a view decorator.
My current project uses Volt in a subsystem containing template creation and editing for special purpose templates. You could do the same with a generic email send subsystem attached to multiple actions across different controllers.