I was just reading this presentation on deploying Drupal

http://www.slideshare.net/eaton/drupal-deployment-presentation

and noticed

http://drupal.org/project/install_profile_api

Which seems to have a collection of API functions needed at install/upgrade time that are missing from Drupal (and contrib modules)

And even better this is great motivation to write more such functions myself instead of just using SQL hacks.