You can try CyberPort in Friedrichstraße (U2, U6 - Stadtmitte) or Gravis (U2 - Ernst-Reuter-Platz) or many of the MediaMarkt or Saturn outlets (Alexanderplatz - U2, U5, U8 or S5 or S7 - has both) to get unlocked iPhones.
Maybe there is even an iPhone store on "Unter den Linden", which is right in the centre of Berlin and not far away from Friedrichstraße.
Also know, that the iPhone 5 is not yet available here as far as it seem.
And avoid the Simon-Dach-Straße, it is full of drunken tourists.
Apple has been "working" on the Apple Store on Kurfürstendamm in Berlin (Germany) for what seems like ages now ... does anyone know when they will finally open it to the public .... IMO it would be god damn stupid not to open in due time to get a part of the X-Mas shopping this year!?!?!?!
I thought they were gonna open it, when the Iphone launched, but I guess they are taking their time. I am honestly really surprised that I haven't seen ANY new products that were introduced in September at the chain stores on display so far. But maybe you will get lucky and snag one up, if not enjoy Berlin