Add a zoomable mini map that remains permanently on one of the corners of the visible desktop so that you can locate where hidden windows are; to go to the specific window just click on the map

Also enable the user to jump to any window by clicking on the mini map plan and be able to change the opaqueness/density of the map so that it doesn't distract from the main windows maybe even have it sitting in the task bar where it opens when you hover your mouse over the icon.