How to upgrade WPMU
Periodically, I and others update the codex entry on how to upgrade WPMU.
If you are going from 2.7 upwards, the easiest thing is to just click the link in the upgrade notice and let it handle it automatically. This works if you’ve made no hacks. If you’ve changed ANY core files, they WILL be overwritten.
Take a backup of your database and wp-content folder before you do anything.
To upgrade between minor versions, you just remove the old files and replace with the new ones, basically. Everything but .htaccess, wp-config.php and the wp-content folder. Compare the new wp-config-sample.php and htaccess.dist to see if any changes were made that you need to apply.