i am creating a base wordpress theme to use as a starting point for all my sites to come.
in my base theme i have a couple custom menus for the heaer and footer.
how can i declare those menus in a way that all my other themes (using the same base) will inherit them?
Use child themes. http://codex.wordpress.org/Child_Themes
Your header.php and other common template parts will be kept in the parent themes and the other files (like page.php, single.php, etc.) will be overriden in the child themes.