Draft plugin example to add a javascript menu into the WP3.5 Media Library popup. Answer to this Wordpress stackexchange question : http://wordpress.stackexchange.com/questions/76980/add-a-menu-item-to-wordpress-3-5-media-manager/

custom_media_menu.js

// for debug : trace every event
/*var originalTrigger = wp.media.view.MediaFrame.Post.prototype.trigger;
wp.media.view.MediaFrame.Post.prototype.trigger = function(){
    console.log('Event Triggered:', arguments);
    originalTrigger.apply(this, Array.prototype.slice.call(arguments));
}*/


// custom state : this controller contains your application logic
wp.media.controller.Custom = wp.media.controller.State.extend({

    initialize: function(){
        // this model contains all the relevant data needed for the application
        this.props = new Backbone.Model({ custom_data: '' });
        this.props.on( 'change:custom_data', this.refresh, this );
    },
    
    // called each time the model changes
    refresh: function() {
        // update the toolbar
    	this.frame.toolbar.get().refresh();
	},
	
	// called when the toolbar button is clicked
	customAction: function(){
	    console.log(this.props.get('custom_data'));
	}
    
});

// custom toolbar : contains the buttons at the bottom
wp.media.view.Toolbar.Custom = wp.media.view.Toolbar.extend({
	initialize: function() {
		_.defaults( this.options, {
		    event: 'custom_event',
		    close: false,
			items: {
			    custom_event: {
			        text: wp.media.view.l10n.customButton, // added via 'media_view_strings' filter,
			        style: 'primary',
			        priority: 80,
			        requires: false,
			        click: this.customAction
			    }
			}
		});

		wp.media.view.Toolbar.prototype.initialize.apply( this, arguments );
	},

    // called each time the model changes
	refresh: function() {
	    // you can modify the toolbar behaviour in response to user actions here
	    // disable the button if there is no custom data
		var custom_data = this.controller.state().props.get('custom_data');
		this.get('custom_event').model.set( 'disabled', ! custom_data );
		
	    // call the parent refresh
		wp.media.view.Toolbar.prototype.refresh.apply( this, arguments );
	},
	
	// triggered when the button is clicked
	customAction: function(){
	    this.controller.state().customAction();
	}
});

// custom content : this view contains the main panel UI
wp.media.view.Custom = wp.media.View.extend({
	className: 'media-custom',
	
	// bind view events
	events: {
		'input':  'custom_update',
		'keyup':  'custom_update',
		'change': 'custom_update'
	},

	initialize: function() {
	    
	    // create an input
	    this.input = this.make( 'input', {
			type:  'text',
			value: this.model.get('custom_data')
		});
		
		// insert it in the view
	    this.$el.append(this.input);
	    
	    // re-render the view when the model changes
	    this.model.on( 'change:custom_data', this.render, this );
	},
	
	render: function(){
	    this.input.value = this.model.get('custom_data');
	    return this;
	},
	
	custom_update: function( event ) {
		this.model.set( 'custom_data', event.target.value );
	}
});


// supersede the default MediaFrame.Post view
var oldMediaFrame = wp.media.view.MediaFrame.Post;
wp.media.view.MediaFrame.Post = oldMediaFrame.extend({

    initialize: function() {
        oldMediaFrame.prototype.initialize.apply( this, arguments );
        
        this.states.add([
            new wp.media.controller.Custom({
                id:         'my-action',
                menu:       'default', // menu event = menu:render:default
                content:    'custom',
				title:      wp.media.view.l10n.customMenuTitle, // added via 'media_view_strings' filter
				priority:   200,
				toolbar:    'main-my-action', // toolbar event = toolbar:create:main-my-action
				type:       'link'
            })
        ]);

        this.on( 'content:render:custom', this.customContent, this );
        this.on( 'toolbar:create:main-my-action', this.createCustomToolbar, this );
        this.on( 'toolbar:render:main-my-action', this.renderCustomToolbar, this );
    },
    
    createCustomToolbar: function(toolbar){
        toolbar.view = new wp.media.view.Toolbar.Custom({
		    controller: this
	    });
    },

    customContent: function(){
        
        // this view has no router
        this.$el.addClass('hide-router');

        // custom content view
        var view = new wp.media.view.Custom({
            controller: this,
            model: this.state().props
        });

        this.content.set( view );
    }

});

custom_media_menu.php

<?php
/*
 * Plugin Name: Custom media menu
 * Description: Adds a custom menu in WP3.5 Media Popup
 * Author: Fabien Quatravaux
 * Version: 1.0
 */

add_action('admin_enqueue_scripts', 'custom_add_script');
function custom_add_script(){
    wp_enqueue_script('custom', plugins_url('custom_media_menu.js', __FILE__), array('media-views'), false, true);
}

add_filter('media_view_strings', 'custom_media_string', 10, 2);
function custom_media_string($strings,  $post){
    $strings['customMenuTitle'] = __('Custom Menu Title', 'custom');
    $strings['customButton'] = __('Custom Button', 'custom');
    return $strings;
}

?>