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To add a menu item to each site of the network if an specific plugin is active in that site, I'm using a Must Use plugin. It only runs if is_multisite() and if is_admin_bar_showing(). There's no user capability checking.

<?php
/**
 * Plugin Name: Modify My Sites admin menu
 * Plugin URI: http://wordpress.stackexchange.com/q/55724/12615
 * Description: Add an admin menu link to specific plugin, if it is active in the site. Can remove default items as well.
 * Author: Rodolfo Buaiz
 * Author URI: http://wordpress.stackexchange.com/users/12615/brasofilo
 * License: GPLv3
 *  
 * Class based in http://wordpress.stackexchange.com/a/77236/12615
 **/

 
WPSE_55724_My_Sites_Extra_Items::init( 
    'Analytics360', // Menu item title
    'analytics360/analytics360.php', // Plugin to check for
    'index.php?page=analytics360.php', // Menu item URL
    array( 'newpost', 'comments', 'visit', 'dashboard' ) // Remove defaults
);

class WPSE_55724_My_Sites_Extra_Items
{
    private static $ins = null;

    private static $title = null;
    private static $plugin_file = null;
    private static $plugin_page = null;
    private static $remove_defaults = null;

    public static function instance()
    {
        is_null( self::$ins ) && self::$ins = new self;
        return self::$ins;
    }

    public static function init( $title, $plugin_file, $plugin_page, $remove_defaults )
    {
        self::$title = $title;
        self::$plugin_file = $plugin_file;
        self::$plugin_page = $plugin_page;
        self::$remove_defaults = $remove_defaults;
        
        if( is_multisite() )
            add_action( 'plugins_loaded', array( self::instance(), '_setup' ) );
    }

    public function _setup()
    {
        if( is_admin_bar_showing() )
            add_action( 'admin_bar_menu', array( $this, 'add_items' ), 9999 );          
    }

    /**
     * The global var is passed by reference in a do_action_ref_array
     */
    public function add_items( $wp_admin_bar ) 
    {
        foreach ( (array) $wp_admin_bar->user->blogs as $blog ) 
        {
            switch_to_blog( $blog->userblog_id );
            
            // Current menu ID
            $menu_id  = 'blog-' . $blog->userblog_id;
            
            // Add URL to current-site/wp-admin/plugins.php
            $wp_admin_bar->add_menu( array(
                'parent' => $menu_id,
                'id'     => $menu_id . '-p',
                'title'  => __( 'Plugins' ),
                'href'   => admin_url( 'plugins.php' ),
            ) );
            
            // Remove default menu items
            $this->remove_items( 
                &$wp_admin_bar, 
                self::$remove_defaults,
                $menu_id
            );
                    
            // Add custom menu for chosen Plugin it active in current site  
            if( current_user_can( 'manage_options' ) && $this->is_plugin_active( self::$plugin_file ))
            {
                $wp_admin_bar->add_menu( array(
                    'parent' => $menu_id,
                    'id'     => $menu_id . '-my-p',
                    'title'  => self::$title,
                    'href'   => admin_url( self::$plugin_page ),
                ) );
            }
                
            restore_current_blog();
        }
    }   

    /**
     * 
     */
    private function remove_items( $wp_admin_bar, $items, $menu_id )
    {
        if( in_array( 'newpost', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-n' ); // New Post

        if( in_array( 'comments', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-c' ); // Comments
            
        if( in_array( 'visit', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-v' ); // Visit Site
            
        if( in_array( 'dashboard', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-d' ); // Dashboard
    }


    /**
     * WP function uses is_plugin_active_for_network 
     * which doesn't work in frontend
     */
    private function is_plugin_active( $plugin )
    {
        return in_array( $plugin, (array) get_option( 'active_plugins', array() ) );
    }
}

To add a menu item to each site of the network if an specific plugin is active in that site, I'm using a Must Use plugin. It only runs if is_multisite() and if is_admin_bar_showing().

<?php
/**
 * Plugin Name: Modify My Sites admin menu
 * Plugin URI: http://wordpress.stackexchange.com/q/55724/12615
 * Description: Add an admin menu link to specific plugin, if it is active in the site. Can remove default items as well.
 * Author: Rodolfo Buaiz
 * Author URI: http://wordpress.stackexchange.com/users/12615/brasofilo
 * License: GPLv3
 *  
 * Class based in http://wordpress.stackexchange.com/a/77236/12615
 **/

 
WPSE_55724_My_Sites_Extra_Items::init( 
    'Analytics360', // Menu item title
    'analytics360/analytics360.php', // Plugin to check for
    'index.php?page=analytics360.php', // Menu item URL
    array( 'newpost', 'comments', 'visit', 'dashboard' ) // Remove defaults
);

class WPSE_55724_My_Sites_Extra_Items
{
    private static $ins = null;

    private static $title = null;
    private static $plugin_file = null;
    private static $plugin_page = null;
    private static $remove_defaults = null;

    public static function instance()
    {
        is_null( self::$ins ) && self::$ins = new self;
        return self::$ins;
    }

    public static function init( $title, $plugin_file, $plugin_page, $remove_defaults )
    {
        self::$title = $title;
        self::$plugin_file = $plugin_file;
        self::$plugin_page = $plugin_page;
        self::$remove_defaults = $remove_defaults;
        
        if( is_multisite() )
            add_action( 'plugins_loaded', array( self::instance(), '_setup' ) );
    }

    public function _setup()
    {
        if( is_admin_bar_showing() )
            add_action( 'admin_bar_menu', array( $this, 'add_items' ), 9999 );          
    }

    /**
     * The global var is passed by reference in a do_action_ref_array
     */
    public function add_items( $wp_admin_bar ) 
    {
        foreach ( (array) $wp_admin_bar->user->blogs as $blog ) 
        {
            switch_to_blog( $blog->userblog_id );
            
            // Current menu ID
            $menu_id  = 'blog-' . $blog->userblog_id;
            
            // Add URL to current-site/wp-admin/plugins.php
            $wp_admin_bar->add_menu( array(
                'parent' => $menu_id,
                'id'     => $menu_id . '-p',
                'title'  => __( 'Plugins' ),
                'href'   => admin_url( 'plugins.php' ),
            ) );
            
            // Remove default menu items
            $this->remove_items( 
                &$wp_admin_bar, 
                self::$remove_defaults,
                $menu_id
            );
                    
            // Add custom menu for chosen Plugin it active in current site or network activated 
            if( current_user_can( 'manage_options' ) && ( $this->is_plugin_active( self::$plugin_file ) || $this->is_plugin_active_for_network( self::$plugin_file ) ) )
            {
                $wp_admin_bar->add_menu( array(
                    'parent' => $menu_id,
                    'id'     => $menu_id . '-my-p',
                    'title'  => self::$title,
                    'href'   => admin_url( self::$plugin_page ),
                ) );
            }
                
            restore_current_blog();
        }
    }   

    /**
     * 
     */
    private function remove_items( $wp_admin_bar, $items, $menu_id )
    {
        if( in_array( 'newpost', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-n' ); // New Post

        if( in_array( 'comments', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-c' ); // Comments
            
        if( in_array( 'visit', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-v' ); // Visit Site
            
        if( in_array( 'dashboard', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-d' ); // Dashboard
    }


    /**
     * WP function uses is_plugin_active_for_network 
     * which doesn't work in frontend
     */
    private function is_plugin_active( $plugin )
    {
        return in_array( $plugin, (array) get_option( 'active_plugins', array() ) );
    }

    private function is_plugin_active_for_network( $plugin )
    {
        $plugins = get_site_option( 'active_sitewide_plugins');
        if ( isset($plugins[$plugin]) )
            return true;
        return false;
    }
}

Haven't found a way of adding the new item, so am rebuilding the menu.

The only caveat is not being able to position the new menu item at the end.

/*
Plugin Name: The Menu Item
Plugin URI: http://wordpress.stackexchange.com/questions/55724/
Description: Add Menu Items to Admin Bar
Version: 1.1
Author: brasofilo
*/

class Brsfl_55724_MenuItem
{

    public function __construct()
    {       
        add_action( 'wp_before_admin_bar_render', array( $this, 'toolbar_link_to_mypage' ), 9999 );
    }

    // http://stackoverflow.com/a/6228630/1287812
    private function contains( $string, array $search, $caseInsensitive=false )
    {
        $exp = '/'.implode('|',array_map('preg_quote',$search)).($caseInsensitive?'/i':'/');
        return preg_match($exp, $string)?true:false;
    }
    
    public function toolbar_link_to_mypage( $wp_admin_bar ) 
    {
        global $wp_admin_bar;
        $the_admin_bar = $wp_admin_bar->get_nodes();
        
        foreach( $the_admin_bar as $key=>$value )
        {
            // Get Only the Blog Nodes
            if( strpos( $key, 'blog-' ) !== false ) 
             {
                // Get Blog ID
                $pos = substr( $key, strpos( $key,'-' ) + 1 );
                
                // Blog Menu Items
                $search_sub_menus = array( '-d','-n','-c','-v' );
                
                // Blog Dashboar Address
                $search_dashboard_url = array( '-d' );
                
                // Remove Each Blog Node and Subnodes
                $wp_admin_bar->remove_node( $key );
                
                 // Grab the Blog Address
                if( $this->contains( $key, $search_dashboard_url ) )
                    $site_url = $value->href;
                    
                // Main Blog Submenu
                if( $this->contains( $key, $search_sub_menus ) ) 
                {
                    $wp_admin_bar->add_node( $value );
                } 
                 // Blogs Sub-submenus
                else 
                 {
                    // Add the Old Node
                    $wp_admin_bar->add_node( $value );
 
                    // Creation of the New Sub-submenu Item
                    $id = 'blog-'.$pos.'-p';
                    $args = array(
                        'id' => $id
                    ,   'parent' => $key
                    ,   'title' => 'My Custom URL'
                    ,   'href' => $site_url.'edit.php?post_type=example'
                    );
                    $wp_admin_bar->add_node($args);
                }
            }
        }
    }   
}

$brsfl_55724_MenuItem = new Brsfl_55724_MenuItem();

^{Answer remade and now working as per the Question specifications.}

To add a menu item to each site of the network if an specific plugin is active in that site, I'm using a Must Use plugin. It only runs if is_multisite() and if is_admin_bar_showing(). There's no user capability checking.

In this example, the plugin is instantiated with the following values that check for the plugin Analytics360º and remove all default menu items:

• Menu item title: Analytics360
• Plugin to check for: analytics360/analytics360.php
• Menu item URL: index.php?page=analytics360.php
• Remove defaults: array( 'newpost', 'comments', 'visit', 'dashboard' )

<?php
/**
 * Plugin Name: Modify My Sites admin menu
 * Plugin URI: http://wordpress.stackexchange.com/q/55724/12615
 * Description: Add an admin menu link to specific plugin, if it is active in the site. Can remove default items as well.
 * Author: Rodolfo Buaiz
 * Author URI: http://wordpress.stackexchange.com/users/12615/brasofilo
 * License: GPLv3
 *  
 * Class based in http://wordpress.stackexchange.com/a/77236/12615
 **/

 
WPSE_55724_My_Sites_Extra_Items::init(  
    'Analytics360', // Menu item title
    'analytics360/analytics360.php', // Plugin to check for
    'index.php?page=analytics360.php', // Menu item URL
    array( 'newpost', 'comments', 'visit', 'dashboard' ) // Remove defaults
); 

class WPSE_55724_My_Sites_Extra_Items
{
    private static $ins = null;

    private static $title = null;
    private static $plugin_file = null;
    private static $plugin_page = null;
    private static $remove_defaults = null;

    public static function instance()
    {
        is_null( self::$ins ) && self::$ins = new self;
        return self::$ins;
    }

    public static function init( $title, $plugin_file, $plugin_page, $remove_defaults )
    {
        self::$title = $title;
        self::$plugin_file = $plugin_file;
        self::$plugin_page = $plugin_page;
        self::$remove_defaults = $remove_defaults;
        
        if( is_multisite() )
            add_action( 'plugins_loaded', array( self::instance(), '_setup' ) );
    }

    public function _setup()
    {
        if( is_admin_bar_showing() )
            add_action( 'admin_bar_menu', array( $this, 'add_items' ), 9999 );           
    }

    /**
     * The global var is passed by reference in a do_action_ref_array
     */
    public function add_items( $wp_admin_bar )  
    {
        foreach ( (array) $wp_admin_bar->user->blogs as $blog ) 
        {
            switch_to_blog( $blog->userblog_id );
             
            // Current menu ID
            $menu_id  = 'blog-' . $blog->userblog_id;
            
            // Add URL to current-site/wp-admin/plugins.php
            $wp_admin_bar->add_menu( array(
                'parent' => $menu_id,
                'id'     => $menu_id . '-p',
                'title'  => __( 'Plugins' ),
                'href'   => admin_url( 'plugins.php' ),
            ) );
             
            // Remove default menu items
            $this->remove_items(  
                &$wp_admin_bar,  
                self::$remove_defaults,
                $menu_id
            );
                    
            // Add custom menu for chosen Plugin it active in current site  
            if( current_user_can( 'manage_options' ) && $this->is_plugin_active( self::$plugin_file ))
            {
                $wp_admin_bar->add_menu( array(
                    'parent' => $menu_id,
                    'id'     => $menu_id . '-my-p',
                    'title'  => self::$title,
                    'href'   => admin_url( self::$plugin_page ),
                ) );
            }
                 
            restore_current_blog();
        }
    }    

    /**
     *  
     */
    private function remove_items( $wp_admin_bar, $items, $menu_id )
    {
        if( in_array( 'newpost', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-n' ); // New Post

        if( in_array( 'comments', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-c' ); // Comments
            
        if( in_array( 'visit', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-v' ); // Visit Site
             
        if( in_array( 'dashboard', $items ) )
            $wp_admin_bar->remove_menu( $menu_id . '-d' ); // Dashboard
    }


    /**
     * WP function uses is_plugin_active_for_network 
     * which doesn't work in frontend
     */
    private function is_plugin_active( $plugin )
    {
        return in_array( $plugin, (array) get_option( 'active_plugins', array() ) );
    }
}

If I understood your question correctly¹, wrapping the action call inside a Class avoids the menu being displayed in all sites of the network.

¹
its only showing when i am in that blog => I understand that you mean: "it is not only showing..."
When i am in blogid:3 or blogid:4, i cant see that menu in blogid:2's list => I understand that you mean: "I can see the menu of blogid:2..."

/*
Plugin Name: The Menu Item
Plugin URI: http://wordpress.stackexchange.com/questions/55724/
Description: Add Menu Items to Admin Bar
Version: 1.0
Author: wordpress.stackexchange
*/

class Brsfl_55724_MenuItem
{

    public function __construct()
    {       
        add_action( 'admin_bar_menu', array($this, 'toolbar_link_to_mypage'), 999 );
    }

    function toolbar_link_to_mypage( $wp_admin_bar ) 
    {
        $menu_id = 'my_page';
        
        $args = array(
            'id'    => $menu_id,
            'title' => 'The Menu Item',
            'href'  => '#',
            'meta'  => array('class' => 'my-toolbar-page')
        );
        
        $args2 =  array(
            'parent' => $menu_id,
            'id'     => $menu_id . '-example',
            'title'  => __( 'Example Menu Item', 'example' ),
            'href'   => get_admin_url( $blog->userblog_id, 'edit.php?post_type=example' ),
            'meta'   => array('class' => 'my-toolbar-page')
        );
        
        $wp_admin_bar->add_node($args);
        $wp_admin_bar->add_node($args2);
    }
    
}
$brsfl_55724_MenuItem = new Brsfl_55724_MenuItem();

Haven't found a way of adding the new item, so am rebuilding the menu.

The only caveat is not being able to position the new menu item at the end.

/*
Plugin Name: The Menu Item
Plugin URI: http://wordpress.stackexchange.com/questions/55724/
Description: Add Menu Items to Admin Bar
Version: 1.1
Author: brasofilo
*/

class Brsfl_55724_MenuItem
{

    public function __construct()
    {       
        add_action( 'wp_before_admin_bar_render', array( $this, 'toolbar_link_to_mypage' ), 9999 );
    }

    // http://stackoverflow.com/a/6228630/1287812
    private function contains( $string, array $search, $caseInsensitive=false )
    {
        $exp = '/'.implode('|',array_map('preg_quote',$search)).($caseInsensitive?'/i':'/');
        return preg_match($exp, $string)?true:false;
    }
    
    public function toolbar_link_to_mypage( $wp_admin_bar ) 
    {
        global $wp_admin_bar;
        $the_admin_bar = $wp_admin_bar->get_nodes();
        
        foreach( $the_admin_bar as $key=>$value )
        {
            // Get Only the Blog Nodes
            if( strpos( $key, 'blog-' ) !== false ) 
            {
                // Get Blog ID
                $pos = substr( $key, strpos( $key,'-' ) + 1 );
                
                // Blog Menu Items
                $search_sub_menus = array( '-d','-n','-c','-v' );
                
                // Blog Dashboar Address
                $search_dashboard_url = array( '-d' );
                
                // Remove Each Blog Node and Subnodes
                $wp_admin_bar->remove_node( $key );
                
                // Grab the Blog Address
                if( $this->contains( $key, $search_dashboard_url ) )
                    $site_url = $value->href;
                    
                // Main Blog Submenu
                if( $this->contains( $key, $search_sub_menus ) ) 
                {
                    $wp_admin_bar->add_node( $value );
                } 
                // Blogs Sub-submenus
                else 
                {
                    // Add the Old Node
                    $wp_admin_bar->add_node( $value );

                    // Creation of the New Sub-submenu Item
                    $id = 'blog-'.$pos.'-p';
                    $args = array(
                        'id' => $id
                    ,   'parent' => $key
                    ,   'title' => 'My Custom URL'
                    ,   'href' => $site_url.'edit.php?post_type=example'
                    );
                    $wp_admin_bar->add_node($args);
                }
            }
        }
    }   
}

$brsfl_55724_MenuItem = new Brsfl_55724_MenuItem();