How To Properly Create Tables In WordPress Multisite Plugins. Explanation at http://sudarmuthu.com/blog/how-to-properly-create-tables-in-wordpress-multisite-plugins/

1.php

<?php
// Creating tables in Single site installations
function on_activate() {
    create_table();
}

function create_table() {
    global $wpdb;
    $table_name = $wpdb->prefix . 'table_name';

    if( $wpdb->get_var( "show tables like '{$table_name}'" ) != $table_name ) {

        $sql = "CREATE TABLE " . $table_name . " (
            id mediumint(9) NOT NULL AUTO_INCREMENT,
            col VARCHAR(100) NOT NULL,
            PRIMARY KEY  (id)
        );";

        require_once( ABSPATH . 'wp-admin/includes/upgrade.php' );
        dbDelta( $sql );

        add_option( EmailLog::DB_OPTION_NAME, EmailLog::DB_VERSION );
    }
}

register_activation_hook( __FILE__, 'on_activate' );
?>

2.php

<?php
// Creating tables for all blogs in a WordPress Multisite installation
function on_activate( $network_wide ) {
    global $wpdb;

    if ( is_multisite() && $network_wide ) {
        // Get all blogs in the network and activate plugin on each one
        $blog_ids = $wpdb->get_col( "SELECT blog_id FROM $wpdb->blogs" );
        foreach ( $blog_ids as $blog_id ) {
            switch_to_blog( $blog_id );
            create_table();
            restore_current_blog();
        }
    } else {
        create_table();
    }
}

register_activation_hook( __FILE__, 'on_activate' );
?>

3.php

<?php
// Creating table whenever a new blog is created
function on_create_blog( $blog_id, $user_id, $domain, $path, $site_id, $meta ) {
    if ( is_plugin_active_for_network( 'plugin-name/plugin-name.php' ) ) {
        switch_to_blog( $blog_id );
        create_table();
        restore_current_blog();
    }
}
add_action( 'wpmu_new_blog', 'on_create_blog', 10, 6 );
?>

4.php

<?php
// Deleting the table whenever a blog is deleted
function on_delete_blog( $tables ) {
    global $wpdb;
    $tables[] = $wpdb->prefix . 'table_name';
    return $tables;
}
add_filter( 'wpmu_drop_tables', 'on_delete_blog' );
?>