Can I trade in my IPhone 4S for an iPhone 5 in an Apple Store and just pay a little extra for the upgrade?

No.

If you bought it in the last week or so, you could return it on the 21st (when Apple Stores will start selling i5) and get the 5. Otherwise, no.

Apple does not do trade-ins.

Try and sell it online and use the cash to pay towards the new phone. There are web sites that will buy your phone and some of them will even let you keep it until you get your new one. But now that the new phone has been announced along with the prices I am pretty sure the price you can get for a used 4 or 4S will have just dropped since what you could have gotten yesterday,.

you can use the recycling program and they give you a gift card for your old iDevice

http://www.apple.com/recycling/gift-card/

you can check an estimate I check my iphone 4s 16gb and it gives $ 255.00

I just heard on the news you can do this. I think the difference is $200