After updating to 3.2.1 (multisite), my Tools menu has disappeared. I only noticed this today as i installed a plugin which placed a menu item in the Tools menu.
How can i get it back? Uninstalling the plugin seems to make no difference, as the Tools menu doesn’t reappear.
Try re-downloading the WordPress files and reinstalling manually them over top of your install. It could be the file that contains the Tools menu was corrupted during installation.