If you are annoyed with this automatic activation of Jetpack modules, specially on a multi-site setup, here is how to completely disable modules across the entire network without having to visit each site and disable modules one by one.Since version 2.4, Jetpack has introduced 'jetpack_get_available_modules' filter, which allows you to black lis…

blacklist_jetpack_modules.php

<?php
/*
Plugin Name: Blacklist Jetpack Modules
Plugin URI: https://gist.github.com/ParhamG/6494979
Description: Blacklist Jetpack modules.
Author: Parham Ghaffarian
Author URI: http://parh.am
Version: 0.1.3.4.1
*/

function blacklist_jetpack_modules( $modules ){
    $jp_mods_to_disable = array(
        // 'shortcodes',
        // 'widget-visibility',
        // 'contact-form',
        // 'shortlinks',
        // 'infinite-scroll',
        // 'wpcc',
        // 'tiled-gallery',
        // 'json-api',
        // 'publicize',
        // 'vaultpress',
        // 'custom-css',
        // 'post-by-email',
        // 'widgets',
        // 'comments',
        // 'minileven',
        // 'latex',
        // 'gravatar-hovercards',
        // 'enhanced-distribution',
        // 'notes',
        // 'subscriptions',
        // 'stats',
        // 'after-the-deadline',
        // 'carousel',
        // 'photon',
        // 'sharedaddy',
        // 'omnisearch',
        // 'mobile-push',
        // 'likes',
        // 'videopress',
        // 'gplus-authorship',
        // 'sso',
        // 'monitor',
        // 'markdown',
        // 'verification-tools',
        // 'related-posts',
        // 'custom-content-types',
        // 'site-icon',
        // 'protect',
    );

    foreach ( $jp_mods_to_disable as $mod ) {
        if ( isset( $modules[$mod] ) ) {
            unset( $modules[$mod] );
        }
    }

    return $modules;
}
add_filter( 'jetpack_get_available_modules', 'blacklist_jetpack_modules' );
?>

Thanks for this awesome snippet.