I successfully installed and configured Tom Willett's Menu Plugin. I found it shortly after I had edited a small piece of Geeklog's internal code in order to add the Blog Links to the Sections menu on the left. I really didn't want to edit it at all because upgrading is a huge pain when you have to port over all of your changes. Luckily it was only a small change and was easy enough to undo.

Anyway, this version of the Menu plugin lets you set up custom menus without changing the core system. It also uses the existing security group heirarchy that you've defined for users. These are Good Things.

It doesn't look any different but it makes my future life much better.