• Open Atrium “an intranet in a box: blog, wiki, calendar, to do list, shoutbox, and dashboard” by DevSeed
• Acquia Drupal by Acquia
• ProsePoint “newspaper content management system”, by Thinkleft
• Pressflow “Drupal with integrated performance, scalability, availability, and testing enhancements” by 4 Kitchens
• Everything under "installation profiles" on Drupal.org

Most of them technically Drupal install profiles.

• Acquia: Drupal Gardens
• Lullabot: Buzzr Enterprise Edition