I've been a long time fan of Mike Lin's excellent Cross Hair app http://www.mlin.net/CrossHair.shtml
I find that about 80% of the time, I'm using it as a reading guide on a webpage or on a CHM help file for an app. When this is the case, I want it to be present only on the given window, not the entire screen.
In the image http://i.imgur.com/KJiRl.png I'm reading item #2 in this help file. I'd like the reading guide (which I've drawn as a gray rectangle) to be associated with this window so that it is only visible over the given window. If I click away from the window (see bottom of image) to work on another window, I want the reading guide to stay in place with the assigned (now inactive) window. It would be like a placeholder for my reading, but also would stay out of my way.
Does that make sense and/or seem like a good idea?