So when I read papers in hard copy, I like to be able to mark the line that I am reading currently using a notecard, which covers up things below the line that I am reading. This keeps me from being distracted. Is there a PDF reader that has a feature like this? I realize that most of the time I could just use the bottom of the screen, but I was just wondering if there is a purpose built tool for this. I use Mac OS X, by the way.
Skim is a free app that should be able to help you with this:
It has a Reading Bar feature that can either highlight one line with a colour of your choice, or highlight all lines but one. You can move the Reading Bar around with your mouse. I hope this helps!