We have some settings that are global for our blogs network, which are enabled by plugins. Problematically, the default behavior for WordPress plugins is to make them available to every site admin, not just to the network super admin.
In the last we have modified our own plugins to change this behavior, but this is more involved than we want to get with the platform.
Admin Menu Editor provides a GUI for this.
If you are a network super-admin, on any of the site dashboards in the network (not the network level dashboard), you can find Menu Editor in the settings menu. In this, for any menu in the admin dashboard, you can set the Extra capability field to "super_admin", which restricts access to network admins only.
It isn't the prettiest solution, because if someone stumbles across the URL and tries to access it they get unhelpful error messages, but it does work. This is bigger issue with plugins like Mail Bank that stick extra branding in the dashboard header, in addition to the menu.