Ryan had the idea, I mused aloud it seemed like it made sense to me, and coming up in the next version of WordPress, everyone who has set up multisite will have the Super admin menu shuffled off into its own area called Network Admin.
In terms of usability, this makes more sense than just an extra box on the left side wherever you are. As a separate admin area, it forces home the idea that the network itself is global and special. When you are in the Network Admin area, the link changes wording to say Site Admin to get back to the site you were on.
If you have a lot of plugins that add menu items to the Super Admin menu, they will now be their own top-level menu item in Network Admin.
Actually, I think this is rather cool, as now you could have whole sections of things pertaining to the entire network in their own handy menu area. Right now things are a little spotty for installed plugins and where the menu items show up. On my test install, some sub menu items that were under Super Admin show up under Settings or even Posts.
Plugin authors may want to do some testing here, especially if your plugin added submenus to the Super Admin menu.
Edit: and since I was looking at trunk, this has already changed. 🙂