If you need to retrieve an instance of a specific window, you have a few different options, each optimal for a given situation. For starters, the main IDE window is always available directly from the
Window IDE = _applicationObject.MainWindow;
Obviously, if you need to perform a specific action against the IDE window, this is your quickest route.
DTE.ActiveWindow property also provides direct and quick access to a
Window object, in this case the currently active window.
Window currentWindow = _applicationObject.ActiveWindow;
The tool windows within the IDE (that is, the Command window, the Error List window, the Output window, the Solution Explorer, ...