Computer-implemented methods for organizing graphical user interface windows into separate stacks of windows is provided are provided. In one aspect, a method includes providing, for display, a first window in a graphical user interface, and receiving a request to display a second window in the graphical user interface when viewing the first window. The method also includes moving the first window to a first stack in the graphical user interface in response to the request, and displaying the second window in the graphical user interface in a second stack. In response to a request to display a third window in the graphical user interface, the third window is configured to be displayed in the first stack or in the second stack based on a defined constraint shared between the third window and the second window. Systems, graphical user interfaces, and machine-readable media are also provided.