Apple has updated their website to reflect that if you want to buy an iPhone 4S at an Apple Store, you're going to have to reserve it online first.
iPhone 4S is available in store by reservation only. Reserve yours after 9:00 p.m. tonight for pickup tomorrow. When you come in, you’ll choose a carrier and plan, and we’ll get your iPhone up and running before you leave the store.
This seems to be Apple's way of minimizing lines and I think it's a great idea. Instead of showing up to the Apple Store hoping that they have some in stock, you can reserve it online the week before.
You can, of course, also order it to be shipped.