In my theme I'd like to have complete control over my menus. I'd like to apply specific classes and wrap the menu however I like. I was thinking I could do this within a template. I see that you can print the menu with this:
<?php $menu = menu_navigation_links('menu-your-custom-menu-name'); print theme('links__menu_your_custom_menu_name', array('links' => $menu)); ?>
But I'm not sure how to edit the individual items within the menu.