There's a module for that! Drupal architecture and module development

UPDATE: The comment by jtsnow resolves the general problem of overriding theme functions in a module using hook_theme_registry_alter(). Woohoo! But the specific problem described below to override the rendering of menu items remains.

I am trying to instruct the menu system to display each item's description underneath the item text, in a smaller font. I located the theme_menu_item() function in menu.inc that currently performs this task.