I have four slots too in my oven. When a recipe calls for the middle one, I use the 2nd one from the bottom as the 2nd from the top is a bit too close to the heating unit. I move the sheet there at the end to broil whatever I'm baking.
And as dragnlaw said above, it also depends on what you are cooking and in what dish. Let's say you're baking a big piece of meat, when you place the sheet on the 2nd rack (from the bottom) the top of the meat would site perfectly in the middle actually