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