Preheat the oven to 325 degrees F.
Trace the pattern you want to make on a sheet of parchment. You can use a simple design or one more intricate, but make sure they image leaves enough room to easily fill the spaces with candy.
Line your patterned parchment into a baking sheet. Use the gingerbread cookie dough to create 1/8-inch thick ropes and lay them over the pattern on the parchment.
Be sure to pinch together any seams so they are strong, especially if you intend to hang the stained glass cookies by ribbon.
Bake the cookie dough for about 3 minutes, just to set it. You don't need to bake it completely, because it will bake further after you've added the candy. Allow the cookie dough to cool completely before adding the candy.
Select the candy you want and crush it into small pieces. Depending on the candy this can be done with a knife, mortar and pestle or food processor.
Arrange the crushed candy in the spaces between the set cookie dough. Make the layers even and bring it as close to the edge as possible.
Bake the cookies for about 5 minutes, until the candies have melted and are smooth. They will be very sticky when hot, but as soon as they cool they will peel right off the parchment.
There is usually a bubble from the candy that will allow you to thread a ribbon in the glass. Don't try to hang it from the cookie edge, because the cookie alone won't be strong enough to hold it up.
To make the gingerbread cookie dough:
In a bowl, whisk together the flour, baking soda, baking powder, salt, ginger, cinnamon, and clove.
In the bowl of a stand mixer cream together the butter and brown sugar with the paddle attachment, until light and fluffy, about 2 minutes on medium-high speed. Scrape down the sides of the bowl. Add the eggs one at a time, mixing well between each and scraping the sides of the bowl. Mix in the molasses on low speed, until well blended. Add the flour all at once and mix on low speed just until it all comes together. Scrape down the bowl and turn the speed to medium, beat for 15 seconds.
Wrap the gingerbread dough in plastic and refrigerate until set up, at least an hour.