Here is a video I'm contributing about configuring a Multisite Drupal install within an Apache server environment.

It provides a number of tips related to optimizing the httpd.conf file for better security on files such as install.php, cron.php and update.php. It also provides tips on managing the multisite configuration by using a dedicated drupal.conf file and controlling access to sensitive areas of the site (like /admin) using an ip.conf file.

One other valuable tip is temporarily using the apache directive DirectoryIndex (while updating drupal) to point all sites managed in the multisite install to a different index page (such as offline.php) so you don't have to go into every site and turn on maintenance mode (which can be a pain).