if ( ! class_exists( 'my_mu_plugin' ) ) {

    if ( function_exists( 'add_action' ) ) {
        add_action( 'plugins_loaded' ,  array( 'my_mu_plugin', 'get_object' ) );
    }

    class my_mu_plugin {

        static private $classobj = NULL;

        public function get_object () {
            if ( NULL === self :: $classobj ) {
                self :: $classobj = new self;
            }
            return self :: $classobj;
        }

        public function __construct () {
            // Fake-Activation-Hook
            $this->activation();
        }

        private function activation () {
            if ( 'activated' == get_blog_option( 1, 'my_mu_plugin_activated' ) ) {
                // Do Stuff during activation
                ...

                // Update Option
                update_blog_option( 1, 'my_mu_plugin_activated', 'activated' );
            }
        }

    }

}

We are doing the following: We check whether a certain option is set in blog 1, if not, then run through an activation function, otherwise do nothing - Blog 1 simple so that the install script is only in blog 1 in use. If you want to use it in all the blogs then simply use the function get_option(). Easy, right?

The following code belongs into a Plugin and should be placed in the folder mu-plugins.

class Add_Blog_ID {

	public static function init() {
		$class = __CLASS__ ;

		if ( empty( $GLOBALS[ $class ] ) )
			$GLOBALS[ $class ] = new $class;
	}

	public function __construct() {

		add_filter( 'wpmu_blogs_columns', array( $this, 'get_id' ) );
		add_action( 'manage_sites_custom_column', array( $this, 'add_columns' ), 10, 2 );
		add_action( 'manage_blogs_custom_column', array( $this, 'add_columns' ), 10, 2 );
		add_action( 'admin_footer', array( $this, 'add_style' ) );
	}

	public function add_columns( $column_name, $blog_id ) {

		if ( 'blog_id' === $column_name )
			echo $blog_id;

		return $column_name;
	}

	// Add in a column header
	public function get_id( $columns ) {

		$columns['blog_id'] = __('ID');

		return $columns;
	}

	public function add_style() {

		echo '<style>#blog_id { width:7%; }</style>';
	}
}
add_action( 'init', array( 'Add_Blog_ID', 'init' ) );

Not easy and probably not an every day task - so that's why I created a small todo list in order not to forget a step to restore to the default installation.

1. Save all your data - Database and files via FTP
2. Set the constant WP_ALLOW_MULTISITE to FALSE or delete the definition
3. Remove the following line in your wp-config.php; Just comment out is enough.

   /**
   define( 'MULTISITE', true );
   define( 'SUBDOMAIN_INSTALL', false );
   $base = '/wordpress/';
   define( 'DOMAIN_CURRENT_SITE', 'localhost' );
   define( 'PATH_CURRENT_SITE', '/wordpress/' );
   define( 'SITE_ID_CURRENT_SITE', 1 );
   define( 'BLOG_ID_CURRENT_SITE', 1 );
   */
   

4. Remove the entries for the network in your .htaccess which is in the root of your installation

   # BEGIN WordPress
   RewriteEngine On
   RewriteBase /wordpress/
   RewriteRule ^index\.php$ - [L]
   
   # uploaded files
   RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]
   
   # add a trailing slash to /wp-admin
   RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]
   
   RewriteCond %{REQUEST_FILENAME} -f [OR]
   RewriteCond %{REQUEST_FILENAME} -d
   RewriteRule ^ - [L]
   RewriteRule  ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
   RewriteRule  ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
   RewriteRule . index.php [L]
   # END WordPress
   

5. Now recreate the permalinks and add the necessary lines to .htaccess (wp-admin/options-permalink.php)
6. Remove the fields spam and deleted in the user-table (adjust prefix)

   ALTER TABLE `wp_users` DROP `spam`, DROP `deleted`;
   

7. You can delete the following tables in your database (adjust prefix)
   • wp_blogs
   • wp_blog_versions
   • wp_registration_log
   • wp_signups
   • wp_site
   • wp_sitemeta
   • wp_sitecategories (if global terms were active)

     DROP TABLE
         `wp_blogs`,
         `wp_blog_versions`,
         `wp_registration_log`,
         `wp_signups`,
         `wp_site`,
         `wp_sitemeta`,
         `wp_sitecategories`;
     

8. Now you have your default installation of your default blog back. But in your database there are still tables of the 2nd created blog. You have to check if you need some information of this former blog. If not, you can also delete the tables of the former 2nd blog.

Just remember: Before proceeding I really recommend to create a backup.

Since WordPress 3.0 is still in development, there might be many changes until the final release.