Is there a way to programmatically locate all Windows within a given application?

I've found a way to do it via reflection on the @hidden WindowManagerGlobal. At least so far I know this works for android-18.

private void logRootViews() {
    try {
        Class wmgClass = Class.forName("android.view.WindowManagerGlobal");                        
        Object wmgInstnace = wmgClass.getMethod("getInstance").invoke(null, (Object[])null);

        Method getViewRootNames = wmgClass.getMethod("getViewRootNames"); 
        Method getRootView = wmgClass.getMethod("getRootView", String.class);
        String[] rootViewNames = (String[])getViewRootNames.invoke(wmgInstnace, (Object[])null);

        for(String viewName : rootViewNames) {
            View rootView = (View)getRootView.invoke(wmgInstnace, viewName);
            Log.i(TAG, "Found root view: " + viewName + ": " + rootView);
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Output:

Found root view: com.example.paintsample/com.example.paintsample.PaintSample/android.view.ViewRootImpl@41deeff0: com.android.internal.policy.impl.PhoneWindow$DecorView{41dcc278 V.E..... R....... 0,0-768,1184}

Found root view: PopupWindow:42887380/android.view.ViewRootImpl@42891820: android.widget.PopupWindow$PopupViewContainer{42891450 V.E..... ........ 0,0-424,618}

Bounty is still up for grabs of course for anyone who can find a better way :)

The Hierarchyviewer tool that comes with the SDK is worth its weight in gold.

I'm not entirely sure this answers the actual question, but it's a better way of getting all root views as suggested in the accepted answer.

As mentioned there, I've also managed to accomplish this only using reflection, except this code supports All versions from API 14 and above (I haven't checked below):

public static List<View> getWindowManagerViews() {
    try {

        if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.ICE_CREAM_SANDWICH &&
                Build.VERSION.SDK_INT < Build.VERSION_CODES.JELLY_BEAN_MR1) {

            // get the list from WindowManagerImpl.mViews
            Class wmiClass = Class.forName("android.view.WindowManagerImpl");
            Object wmiInstance = wmiClass.getMethod("getDefault").invoke(null);

            return viewsFromWM(wmiClass, wmiInstance);

        } else if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.JELLY_BEAN_MR1) {

            // get the list from WindowManagerGlobal.mViews
            Class wmgClass = Class.forName("android.view.WindowManagerGlobal");
            Object wmgInstance = wmgClass.getMethod("getInstance").invoke(null);

            return viewsFromWM(wmgClass, wmgInstance);
        }

    } catch (Exception e) {
        e.printStackTrace();
    }

    return new ArrayList<View>();
}

private static List<View> viewsFromWM(Class wmClass, Object wmInstance) throws Exception {

    Field viewsField = wmClass.getDeclaredField("mViews");
    viewsField.setAccessible(true);
    Object views = viewsField.get(wmInstance);

    if (views instanceof List) {
        return (List<View>) viewsField.get(wmInstance);
    } else if (views instanceof View[]) {
        return Arrays.asList((View[])viewsField.get(wmInstance));
    }

    return new ArrayList<View>();
}