The bigger Apple stores usually don't run out for the entire weekend, but that's where you'll have to spend several hours in line.
I suggest waiting for Friday afternoon. From what I've seen in the past, the people that get there at midnight end up leaving around 10 AM (so, 10 hours of waiting time) whereas the people who come at 4 PM end up leaving by 8 PM. I've done it both ways and that's generally what I've seen each year.
I've done early morning and 'after work' and waiting for the afternoon is always more pleasant...assuming they don't run out of the phone you want. I have the luck of being near a large flagship store. I think that helps. If you're going to a big city store I suggest just going later.
It's a small risk that you won't get a phone, but you're likely to put in far fewer hours in line and in the past I've still had luck in the afternoon.