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.

Everybody who had the uninstall function in their Plugin, doesn’t have to change a lot. For everybody who likes to know, you can find the function for uninstall in wp-admin/includes/plugin.php

1. is_uninstallable_plugin($plugin)
2. uninstall_plugin($plugin)

and the associated hook wp-includes/plugin.php

1. register_uninstall_hook($file, $callback)

You can use two possibilities to add the additional function.

1. A file with the name uninstall.php has to be in the Plugin.
2. A hook for uninstall register_uninstall_hook has to talk to.

Up to Version 2.7 you were also able to delete the data from the database, but only if you deactivated the Plugin (Hook register_deactivation_hook()) or with help of a formular.

To use also other versions of WordPress, I suggest to use the constant WP_UNINSTALL_PLUGIN, because this one exists in version 2.7. Alternative you can use the hook register_uninstall_hook(), since this one is necessary to function via hook. Both possibles are listed in the following examples.

The following function for example should be in the Plugin and deleting the entry example from the database table options.

/**
 * Delete options in database
 */
function example_deinstall() {

	delete_option('example');
}

via Data uninstall.php

Easiest possibility is to create the file unistall.php with according entries to delete data in the table options.

delete_option('example');

To avoid an error in older WordPress versions, I recommend to use a constant. Isn’t there a constant defined, it will just stop in this example.

if ( !defined('WP_UNINSTALL_PLUGIN') ) {
    exit();
}
delete_option('example');

via hook register_uninstall_hook()

Alternatively you can register the deinstallation via hook, so that you are not depend on the file and you can use a easier possibility to integrate an uninstallation in your Plugin. For that you can use the hook register_uninstall_hook().

 /**
 * Check for hook
 */
if ( function_exists('register_uninstall_hook') )
	register_uninstall_hook(__FILE__, 'example_deinstall');

 /**
 * Delete options in database
 */
function example_deinstall() {

	delete_option('example');
}

The possibility, to delete Plugins directly in your backend, certainly makes it easier for the user to get rid off unused data. But for that, the Plugin authors have to support this feature and the table options certainly will be thankful for that.