The perspective granted by a shadow box gives a sense of looking in on a world that a flat picture just doesn't. Take a look, for instance at this piece by Pixel Eyes Art, that brings the SNES's Legend of Zelda map to life.
Click the images to make them larger.
Both the light world:
And the dark:
Pixel Eyes Art looks to be focused wholly on shadow boxes, though not just on making maps. He's also made old NES game covers:
And taken scenes from games across the generations of Nintendo games:
You can look over Pixel Eyes Art's other projects on his blog.