a very simple bootstrap boilerplate for building backbone.marionette based on require.js

app.js file

   define([

  'jquery',
  'underscore',
  'backbone',
  'marionette', 
  'handlebars',
  'text!templates/app_view.html',

  'modules/mainMenuView/mainMenuView',
  'modules/dashboard/dashboard',
],
function ($, _, Backbone, Marionette, Handlebars, tmpl, mainMenuView, dashboard ) {


    Backbone.Marionette.TemplateCache.prototype.compileTemplate = function(rawTemplate) {

        return Handlebars.compile(rawTemplate);
    };

    var App = new Backbone.Marionette.Application();

    App.addRegions({

         main: '#main'
    });

    App.addInitializer(function() {

       this.initAppLayout();   
    });

    App.on("initialize:after", function(){

      Backbone.history.start({ pushState: true });
    });

    App.initAppLayout = function() {

        AppLayout = Backbone.Marionette.Layout.extend({

         template: tmpl,

         regions: {
             userInfo: "#userInfo",
             mainMenu: "#mainMenu",
             content: "#content"
         },

        });

        var layout = new AppLayout();
        App.main.show(layout);

        App.main.currentView.mainMenu.show(new mainMenuView.Views.menu());
        App.main.currentView.content.show(new dashboard.Views.main());    

       // this can be a main menu navigation
       // this will change content at the "main" app screen
       // your links should include the role=nav-main-app

        $('a[role=nav-main-app]').click(function(e) {
          App.Router.navigate( $(this).attr('href'), {trigger: true});
          e.preventDefault(); 
        });  

    };

    return App;

});

app.js file:

   define([

  'jquery',
  'underscore',
  'backbone',
  'marionette', 
  'handlebars',
  'text!templates/app_view.html',

  'modules/mainMenuView/mainMenuView',
  'modules/dashboard/dashboard',
],
function ($, _, Backbone, Marionette, Handlebars, tmpl, mainMenuView, dashboard ) {


    Backbone.Marionette.TemplateCache.prototype.compileTemplate = function(rawTemplate) {

        return Handlebars.compile(rawTemplate);
    };

    var App = new Backbone.Marionette.Application();

    App.addRegions({

         main: '#main'
    });

    App.addInitializer(function() {

       this.initAppLayout();   
    });

    App.on("initialize:after", function(){

      Backbone.history.start({ pushState: true });
    });

    App.initAppLayout = function() {

        AppLayout = Backbone.Marionette.Layout.extend({

         template: tmpl,

         regions: {
             userInfo: "#userInfo",
             mainMenu: "#mainMenu",
             content: "#content"
         },

        });

        var layout = new AppLayout();
        App.main.show(layout);

        App.main.currentView.mainMenu.show(new mainMenuView.Views.menu());
        App.main.currentView.content.show(new dashboard.Views.main());    

       // this can be a main menu navigation
       // this will change content at the "main" app screen
       // your links should include the role=nav-main-app

        $('a[role=nav-main-app]').click(function(e) {
          App.Router.navigate( $(this).attr('href'), {trigger: true});
          e.preventDefault(); 
        });  

    };

    return App;

});

config.js file

// Use ECMAScript 5 Strict Mode
"use strict";

// Define jQuery as AMD module
define.amd.jQuery = true;

// Set the require.js configuration for your application.
require.config({

  // Initialize the application with the main application file
  deps: ["main"],

  paths: {

    libs: "../assets/js/libs",
    plugins: "../assets/js/plugins",

    // Libraries
    jquery: "../assets/js/libs/jquery",
    underscore: "../assets/js/libs/lodash",
    backbone: "../assets/js/libs/backbone",
    marionette: "../assets/js/libs/backbone.marionette",
    handlebars: "../assets/js/libs/handlebars",

    //plugins
    text : "../assets/js/plugins/text",
    i18n : "../assets/js/plugins/i18n",
    cookie: '../assets/js/plugins/jquery.cookie',

    //general
    UserSession: "../assets/js/libs/userSession",
  },

  config: {
        //Set the config for the i18n
        //module ID
        i18n: {
            locale: 'fr-fr'
        }
    },

  shim: {

     marionette: {
      deps: ['backbone'],
      exports: 'Backbone.Marionette'
    },

    backbone: {
      deps: ["underscore", "jquery"],
      exports: "Backbone"
    },

    handlebars: {
      deps: [],
      exports: "Handlebars"
    }

  }
});

config.js file:

// Use ECMAScript 5 Strict Mode
"use strict";

// Define jQuery as AMD module
define.amd.jQuery = true;

// Set the require.js configuration for your application.
require.config({

  // Initialize the application with the main application file
  deps: ["main"],

  paths: {

    libs: "../assets/js/libs",
    plugins: "../assets/js/plugins",

    // Libraries
    jquery: "../assets/js/libs/jquery",
    underscore: "../assets/js/libs/lodash",
    backbone: "../assets/js/libs/backbone",
    marionette: "../assets/js/libs/backbone.marionette",
    handlebars: "../assets/js/libs/handlebars",

    //plugins
    text : "../assets/js/plugins/text",
    i18n : "../assets/js/plugins/i18n",
    cookie: '../assets/js/plugins/jquery.cookie',

    //general
    UserSession: "../assets/js/libs/userSession",
  },

  config: {
        //Set the config for the i18n
        //module ID
        i18n: {
            locale: 'fr-fr'
        }
    },

  shim: {

     marionette: {
      deps: ['backbone'],
      exports: 'Backbone.Marionette'
    },

    backbone: {
      deps: ["underscore", "jquery"],
      exports: "Backbone"
    },

    handlebars: {
      deps: [],
      exports: "Handlebars"
    }

  }
});

controller.js file

define([
  'jquery',
  'underscore',
  'backbone',
  'marionette',
  'app',
  'userSession'
], 
function($, _, Backbone, Marionette, App, userSession) {

    return {

        goto_path1: function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul1'], function(someview){

                var currentView = new someview.Views.main();
                App.main.currentView.content.show(currentView);          
          })
        },

         goto_path2:  function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul2'], function(someOtherview){

                var currentView = new someOtherview.Views.main();
                App.main.currentView.content.show(currentView);    
            })
        },
        isAuthenticated: function() {

          if(!userSession.authenticated()){
               App.Router.navigate('login', {trigger: true});
           }
        }

    }   

});

controller.js file

  define([
  'jquery',
  'underscore',
  'backbone',
  'marionette',
  'app',
  'userSession'
], 
function($, _, Backbone, Marionette, App, userSession) {

    return {

        goto_path1: function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul1'], function(someview){

                var currentView = new someview.Views.main();
                App.main.currentView.content.show(currentView);          
          })
        },

         goto_path2:  function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul2'], function(someOtherview){

                var currentView = new someOtherview.Views.main();
                App.main.currentView.content.show(currentView);    
            })
        },
        isAuthenticated: function() {

          if(!userSession.authenticated()){
               App.Router.navigate('login', {trigger: true});
           }
        }

    }   

});

controller.js file:

define([
  'jquery',
  'underscore',
  'backbone',
  'marionette',
  'app',
  'userSession'
], 
function($, _, Backbone, Marionette, App, userSession) {

    return {

        goto_path1: function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul1'], function(someview){

                var currentView = new someview.Views.main();
                App.main.currentView.content.show(currentView);          
          })
        },

         goto_path2:  function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul2'], function(someOtherview){

                var currentView = new someOtherview.Views.main();
                App.main.currentView.content.show(currentView);    
            })
        },
        isAuthenticated: function() {

          if(!userSession.authenticated()){
               App.Router.navigate('login', {trigger: true});
           }
        }

    }   

});

controller.js file:

  define([
  'jquery',
  'underscore',
  'backbone',
  'marionette',
  'app',
  'userSession'
], 
function($, _, Backbone, Marionette, App, userSession) {

    return {

        goto_path1: function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul1'], function(someview){

                var currentView = new someview.Views.main();
                App.main.currentView.content.show(currentView);          
          })
        },

         goto_path2:  function () {

            this.isAuthenticated();
            require(['modules/files/files_for_modul2'], function(someOtherview){

                var currentView = new someOtherview.Views.main();
                App.main.currentView.content.show(currentView);    
            })
        },
        isAuthenticated: function() {

          if(!userSession.authenticated()){
               App.Router.navigate('login', {trigger: true});
           }
        }

    }   

});

index.html

<!doctype html>
<html lang="en">
<head>
  <meta charset="utf-8">
  <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
  <meta name="viewport" content="width=device-width,initial-scale=1">

  <title>Backbone.js</title>

  <!-- Application styles -->
  <!-- <link rel="stylesheet" href="/assets/css/index.css"> -->
  <!-- Frameworks -->
  <link rel="stylesheet" href="assets/css/bootstrap.min.css">
  <link rel="stylesheet" href="assets/css/bootstrap-responsive.min.css">
  
</head>

<body>
  <!-- Main container -->
  <div role="main" id="main"></div>

  <!-- Application source -->
  <script data-main="app/config" src="assets/js/libs/require.js"></script>
</body>
</html>

main content template

<div id="main-layout" type="layout">
	
	<div class="container-fluid">
		
	  <div class="row-fluid">
	  	
	    <div class="span2" >
	      <!--Sidebar content-->
	      <nav id="mainMenu" class="mainMenu">menu</nav>
	    </div>
	    
	    <div class="span10">
	    	
	    	<div >
		      <!--Body content-->
		       <header id="userInfo" class="userInfo">header</header>
	        </div>

	     
	      <!--Body content-->
	      <div style="height: 500px;background-color: #f2f2f2">
	      		<section id="content" class="content"></section>
	      </div>
	       
	      <!--Body content-->
	      <div >
		      <footer id="footer" class="footer">
			  	 <p>VERSION:1.1</p>
			   
		  	  </footer>
	     </div>
	      
	    </div>
	    
	  </div> 
	  
	</div>
	
</div>

main.js file

   define([
    "jquery", 
    "app", 
    "router",
    'userSession'
],
function ($, App, router,userSession) {

  "use strict";

  $(function() {

    App.Router = router; 
    App.start();


   // if(userSession.authenticated())
       //alert("us");


  });

});

main.js file:

   define([
    "jquery", 
    "app", 
    "router",
    'userSession'
],
function ($, App, router,userSession) {

  "use strict";

  $(function() {

    App.Router = router; 
    App.start();


   // if(userSession.authenticated())
       //alert("us");


  });

});

nav template

<section id="menu">
	
  <h1>Contents</h1>

  <ul>
    <li><a href="dashboard" role="nav-main-app">DASHBOARD</a></li>
    <li><a href="reports" role="nav-main-app">REPORTS</a></li>
    <li><a href="payments" role="nav-main-app">PAYMENTS</a></li>
    <li><a href="settings" role="nav-main-app">SETTINGS</a></li>
  </ul>
  
  
 
</section>

some html template using handlebars

<div>
	dashboard
	
	<div class="hero-unit">
		  <h1>Heading</h1>
		  <p>Tagline</p>
		  <p>
		  	<div>{{ok}}</div>
				<div>{{cancel}}</div>
				<div>{{this.feedUrl}}</div>
		    <a class="btn btn-primary btn-large">
		        
		    </a>
		  </p>
	</div>
</div>

userSession.js file

  define([
     'jquery',
     'underscore',
      'backbone',
      'cookie'
    ],
function($, _, Backbone, cookie){

    var UserSession = Backbone.Model.extend({

        defaults: {

            'accessToken': null,
            'userId': null
        },

        initialize: function(){

            this.load();
        },

        authenticated: function(){

            return Boolean(this.get('accessToken'));
        },

        save: function(authHash){

            $.cookie('userId', authHash.id);
            $.cookie('accessToken', authHash.accessToken);
        },

        load: function(){

            this.userId = $.cookie('userId');
            this.accessToken = $.cookie('accessToken');
        }
    })

    return new UserSession();

});

userSession.js file:

  define([
     'jquery',
     'underscore',
      'backbone',
      'cookie'
    ],
function($, _, Backbone, cookie){

    var UserSession = Backbone.Model.extend({

        defaults: {

            'accessToken': null,
            'userId': null
        },

        initialize: function(){

            this.load();
        },

        authenticated: function(){

            return Boolean(this.get('accessToken'));
        },

        save: function(authHash){

            $.cookie('userId', authHash.id);
            $.cookie('accessToken', authHash.accessToken);
        },

        load: function(){

            this.userId = $.cookie('userId');
            this.accessToken = $.cookie('accessToken');
        }
    })

    return new UserSession();

});

<!doctype html>

<title>Backbone.js</title>

<script data-main="app/config" src="assets/js/libs/require.js"></script>

Thank you for this wonderful boilerplate. I think is the simplest and the best one out there.
If possible please add module view files. This will make boilerplate complete.

THANK YOU FOR SHARE ! But if the module view is the Marionette module?