Allow WordPress users to log in to wp-admin and wp-login.php while in maintenance mode. Stick this in your web root to put your site into maintenance mode.

.maintenance

<?php
function is_user_logged_in() {
  $loggedin = false;
	foreach ( (array) $_COOKIE as $cookie => $value ) {
		if ( stristr($cookie, 'wordpress_logged_in_') )
			$loggedin = true;
	}
	return $loggedin;
}
if ( ! stristr($_SERVER['REQUEST_URI'], '/wp-admin') && ! stristr($_SERVER['REQUEST_URI'], '/wp-login.php') && ! is_user_logged_in() )
	$upgrading = time();
?>