Is it possible to take simultaneous screenshots of two windows? I want to be able to take a screenshot of two windows at the same time without capturing what's in the background. For instance, instead of taking a picture like this:
  

I want a picture like this:

Obviously it was quickly Photoshopped, but you get the point.
So is this possible?
You could use Layers - it screenshots the entire screen but saves each object in a separate layer. You then export to PSD or a set of .png (or .tiff) images