This plugin contains many examples of how to change different blog defaults. This plugin contains no user interface at the moment, so you will need to edit the plugin for the desired changes. They can be enabled/disabled by commenting out the filter/action below the function.

Features include:
-Hiding submenus
-Default post permalink structure
-Default blogroll links
-Default widgets
-Comment moderation settings
-Mailing settings
-Header navigation links

Homepage: WPMU Blog Defaults