I came across your TurnKey website yesterday. Since I was already experimenting with VirtualBox, I decided to download and test the Drupal appliance. The process went smoothly and in a few minutes I had a working website. One of Drupal's shortcomings (IMHO) is the difficulty of updating modules and the core software. The situation improves with each new version, but right now the best tool I've found is drush, short for drupal shell. Drush update will download and apply module updates, and hopefully soon be able to upgrade core. Drush has a number of useful administrative commands. I was able to install Drush on the Drupal appliance and so far it appears to work quite well. I would highly recommend you consider including Drush in future additions of the Drupal appliance. I've documented the necessary steps if you are interested. Drush can be found at http://drupal.org/project/drush.
Note: Edited InstallDrush.txt on 1/23/10 to change php-cli to php5-cli, use /tmp instead of /opt, and cleanup after.
Note: Edited on 4/25/10 to correct path error reported by Johnny Canuck.
Note: Edited on 6/6/10 to correct symlink error reported by Dan.