Both the_header and the_footer functions except a $name argument which allows you to specify other headers than the default header.php and footer.php.
<?php get_header( 'special' ); ?>
WordPress would then look for header-special.php in your theme directory. If you want to specify a different footer file it works the same way.
I rarely see it used but it can be quite useful, perhaps if you want a “clean” header with just the <html> and <head>.