I'd say it's used in server side code to look for %%SUBMENU%% and replace it with the actual sub menu that is probably built dynamically from a database.
I use $$$SUBMENU$$$ to do my replaces. They are placemarks in the template so I know where to put the sub menu.
It might have gotten outputted on to the page because they forgot to replace it or something.
Here's my raw template file:
$$$PAGETITLE$$$
but all the placemarkers get replaced on the actual pages of the site.
Hope that explains it.
Dave