Behold the magic of Gallery Glass Window Color! Found this paint in the glass tiles/stained glass section at Hobby Lobby. The paint becomes more translucent as it dries. The photos show the dry state (above) and the wet state (below) of the paint.
I would suggest painting the windows before assembly, but if you have already finished your house, don't despair! The paint is thick enough to paint the windows at an upright position and dripping can be avoided if you are a little careful. The Gallery Glass paints come in an array of colors. I have used teal and harvest yellow for my manor.