1. Photo galleries:
I think there are nearly 90 galleries in Berlin, but they arise as fast as they disappear.
For a brief list look here
"photo galleries in Berlin 07/2012"
The galleries, that are probably best known in Berlin are: C/O Berlin,camerawork,Museum fuer Fotografie,Berlinische Galerie
2. Second hand stores and markets
For a brief list look also here
"shops used for cameras and objective"
The question is, what you are looking for ?
If your looking for used equipment and a bargain or cheap stuff goto photo Stade, Foto Schilling, ASA90, Foto Hess and Kamera Objektiv (btw and you should be really careful, But with a little luck you can find a veritable treasure)
if your looking for used equipment with a warranty visit Leistenschneider or Foto Hess.
The remaining shops on the list you will sell new equipment, including Leistenschneider and Foto Hess.
3. Book stores
Goto
"Bücherbogen" - The book shop is a specialist on art and has the largest selection or goto
"Buchhandlung Walter König"
this bookstore is extremely well sorted and has some rare editions.
4. Coffee shops
Throw a stone in any direction, follow the draft direction and you are bound to find a coffee shop faster than you think.
5. Small museums - a bit away from the large "tourist magnets"
Sorry, I have to ask again, what are you looking for and what you're interested.
Greetings from Berlin