The wordpress.org infrastructure work has reminded me how much I dislike having the Super Admin/Network Admin pages appearing alongside the regular per-blog admin pages. I think the Super Admin menu should go away, away to a separate network admin area. Ticket 14435 is where I’m scratching this itch. The patches there move the network admin pages to wp-admin/network/. It is a completely separate admin area just for network management. It is available only from the main site url. Visiting wp-admin/network from other blogs in the network will redirect to the one true place. If you have multiple networks, they each will have a network admin area.
While I was in there I added a network plugins.php. Network activations and deactivations happen here and only here. Network activate/deactivate is no longer available from the blog admins.