Love the place, I've been visiting Berlin three times a year past few years.
Here's some tips that I can remember:
Great photography gallery C/O Berlin
http://www.co-berlin.info/
Nice vietnamese to pop while shopping in Burg & Schild and 14 oz
http://www.monsieurvuong.de/
And a MUST visit every time is a pizzeria run by italian punkrockers
I Due Forni http://www.tripadvisor.com/Restaurant_Review-g187323-d886780-Reviews-I_Due_Forni-Berlin.html
(they also have two more of these restaurants, Il Ritrovo in Friedrichshain and one in Kreuzberg)
Great japanese restaurant Sasaya in Prenzlauer Berg
http://sasaya-berlin.de/
White Trash is the place to get some beer and good food
http://www.whitetrashfastfood.com/
Alpenstück was nice
http://www.alpenstueck.de
Cocolo was recommended by Daniel of DC4 but didn't have the time to go there on last visit
http://www.qype.com/place/362605-Cocolo-ramen–Berlin
On sunday, you should visit fleamarkets in Mauerpark and Arkonaplatz
http://berlin.barwick.de/shopping/flea-markets/flohmarkt-am-mauerpark.html
http://berlin.barwick.de/shopping/flea-markets/flohmarkt-am-arkonaplatz
Bike is the best way to get around in Berlin, lots of places to rent one too. Lila Bike is cheap and reliable http://www.berlin-citytours-by-bike.de/
Some random links:
Rembetis, old bikes
http://www.rembetis1.de/
Manufactum, all things hand made
http://www.manufactum.de/Kategorie/-41/Berlin.html
Berlin underground tours
http://berliner-unterwelten.de/
