We're currently evaluating some way to categorize and break up the secondary contextual nav. In more than one of our pilot courses there were so many tools added that it became a usability issue. Grouping the links in some default way is one project we're currently tackling. Beyond that, we're considering letting our users create proprietary categories for their tools. We're also working functionality to let users modify the link names. We've identified tool/link editing as a gap for our Blackboard to Sakai migration path.
We haven't 100% established what links would be uneditable vs. editable and the usability implications of functionality vs. familiarity and consistent user experience.
Has anyone else come across similar issues or requirements?