Basically the rule is "don't be a dick". Hard to quantify. I've seen coffee shops around college campuses close, because students would come in as a study group, buy $3 worth of coffee, then hog the best seats for 4 hours. Customers come in, no place to sit, turn around and leave. This happens over and over. During the busy evening or morning hours. Yeah after a while the barista can try to politely ask you to move or leave, but if they reach that point, it is already kind of unpleasant both for you and for them.

If the place is almost empty, you'd actually be doing them a favor probably by sitting in there to make the place look popular and happening (those that don't know the place might skip it as well if they see it completely empty).