Let's say you are in an application and have some scripts that are relevant to that application. The user, developer, or packager can add these custom commands to the HUD for that particular application (or set of applications), which become searchable just like any other menu item.
(may also be a good idea to add this to the mate-appmenu applet)
The result would be an customizable and searchable command pallete (like "emacs-helm") for the entire desktop.