Set application menu would set menu for all windows on Windows.

browser/api/lib/menu-item.coffee

@@ -1,3 +1,5 @@
+BrowserWindow = require 'browser-window'
+
 nextCommandId = 0
 
 class MenuItem
@@ -26,7 +28,7 @@ class MenuItem
     @commandId = ++nextCommandId
     @click = =>
       if typeof click is 'function'
-        click.apply this, arguments
+        click this, BrowserWindow.getFocusedWindow()
       else if typeof @selector is 'string'
         Menu.sendActionToFirstResponder @selector
 

browser/api/lib/menu.coffee

@@ -3,6 +3,7 @@ EventEmitter = require('events').EventEmitter
 IDWeakMap = require 'id-weak-map'
 MenuItem = require 'menu-item'
 
+app = require 'app'
 bindings = process.atomBinding 'menu'
 
 Menu = bindings.Menu
@@ -39,7 +40,7 @@ Menu::insert = (pos, item) ->
       getAcceleratorForCommandId: (commandId) => @commandsMap[commandId]?.accelerator
       executeCommand: (commandId) =>
         activeItem = @commandsMap[commandId]
-        activeItem.click(activeItem) if activeItem?
+        activeItem.click() if activeItem?
   @items.splice pos, 0, item
   @commandsMap[item.commandId] = item
 
@@ -47,7 +48,12 @@ applicationMenu = null
 Menu.setApplicationMenu = (menu) ->
   throw new TypeError('Invalid menu') unless menu?.constructor is Menu
   applicationMenu = menu  # Keep a reference.
-  bindings.setApplicationMenu menu
+
+  if process.platform is 'darwin'
+    bindings.setApplicationMenu menu
+  else
+    windows = app.getBrowserWindows()
+    w.setMenu menu for w in windows
 
 Menu.sendActionToFirstResponder = bindings.sendActionToFirstResponder
 

spec/main.js

@@ -1,6 +1,7 @@
 var app = require('app');
 var ipc = require('ipc');
 var BrowserWindow = require('browser-window');
+var Menu = require('menu');
 
 var window = null;
 
@@ -39,6 +40,42 @@ app.on('window-all-closed', function() {
 });
 
 app.on('finish-launching', function() {
+  var template = [
+    {
+      label: 'File',
+      submenu: [
+        {
+          label: 'Open',
+          accelerator: 'Command+O',
+        },
+        {
+          label: 'Close',
+          accelerator: 'Command+W',
+          click: function(item, window) { window.close(); }
+        },
+      ]
+    },
+    {
+      label: 'View',
+      submenu: [
+        {
+          label: 'Reload',
+          accelerator: 'Command+R',
+          click: function(item, window) { window.restart(); }
+        },
+        {
+          label: 'Enter Fullscreen',
+          click: function(item, window) { window.setFullScreen(true); }
+        },
+        {
+          label: 'Toggle DevTools',
+          accelerator: 'Alt+Command+I',
+          click: function(item, window) { window.toggleDevTools(); }
+        },
+      ]
+    },
+  ];
+
   // Test if using protocol module would crash.
   require('protocol').registerProtocol('test-if-crashes', function() {});
 
@@ -49,4 +86,7 @@ app.on('finish-launching', function() {
     height: 600
   });
   window.loadUrl('file://' + __dirname + '/index.html');
+
+  var menu = Menu.buildFromTemplate(template);
+  app.setApplicationMenu(menu);
 });