You need to de-register the existing query and re-register it to load in the footer.
function jquery_in_footer() {
if (!is_admin()) {
wp_deregister_script('jquery');
wp_register_script('jquery', home_url(trailingslashit(WPINC) . 'js/jquery/jquery.js'), false, null, true);
wp_enqueue_script('jquery');
}
}
add_action('init', 'jquery_in_footer');
Bear in mind that if you have any other scripts enqueued that depend on jQuery and are not loaded in the footer, WordPress will still load jQuery in the header to satisfy that dependency.
(adapted from http://www.ericmmartin.com/5-tips-for-using-jquery-with-wordpress/)
Edit: If you really want to get crazy, you could modify the WP_Scripts object directly, but then you're dependent on the implementation never changing. I imagine that would change before they even thought of moving jquery.js' location in wp-includes :)
But just for fun…
function load_jquery_footer() {
global $wp_scripts;
$wp_scripts->in_footer[] = 'jquery';
}
add_action('wp_print_scripts', 'load_jquery_footer');