For our game Flicker of Hope (formerly WICK), we knew we wanted stained glass for the chapel/cathedral setting. The process was a collaboration between me as a TA and Niara Clay for the window designs and models.
The light through the glass is done using light functions on a series of spotlights. We had considered using decals, but the prevalence of rubble and debris on the floor would have likely led to odd stretching artifacts and issues, so we pivoted to the light function method.
Glass in action