When using chrome developer tools, it appears that each app window (and the background \'page\') has its own javascript context (space of objects, thread of execution), and
You might find the chrome.app.window.getAll() and chrome.app.window.get() methods useful. They are however new to Chrome 33 which is not yet in the stable channel.
As an alternative you could hold an array of opened AppWindow objects in the background page context.
You can then get a reference to the background page context from any window using the chrome.runtime.getBackgroundPage() method