I think custom variables were originally designed to be used in emails but I use them within the main site for little bits of information whose value needs to change on a per store/language basis.
This is how you get a custom variable inside a phtml file:
You can create and set these custom variables in the admin via the system>custom variable menu. Note that you can’t set values for different stores/languages until you have saved your initial value. Going in to edit it once saved will allow you to change the values per store.
I use this as a sort of cheaters way of having some controllable values available in the admin without creating proper configuration values in modules and that sort of thing.