I had a fat encyclopedia as a kid that illustrated the human anatomy with stacked, transparent overlays. The top was an illustration of a man. Pull it back and it was the muscles. Pull it back and there were the arteries and veins. Pull it back and see the bones. It captivated me.
What if we used a similar idea on maps?
The problem is that the home printers we're using are limited in the colors they'll print and they aren't capable of a truly solid color. My encyclopedia used something more like cell animation, with layers higher in the stack, meant to obscure, painted solid. Screenprinting could do this, if the ink would stick to clear vinyl and if the vinyl would hold up to the 350 degree F curing my plastisol inks require.
But we might still be able to make something cool with just black line printing on transparencies.
Think of your campaign map, any extra "layer" of information you would like to incorporate could become a literal layer overlaid: trade routes, trade goods, demi-human demographics, religions, climate zone, etc.
Or, at a closer scale, a transparent overlay might be handy for a dungeon/location that goes through changes that are hard to keep track of. Time travel. The players get a hold of some way to travel through time and you can flip your overlays of the manor and surrounding region to show how things get built up as they bounce back and forth.
Or, here are two ideas that are exciting me the most 1) an overlay to use on my hex geomorphs to represent a special, like a stream crossing the geomorph 2) the sinking dungeon at various water depths.