During my week stay in Berlin I managed about 8 museums and art spaces. There's quite a bit happening with something like 600 galleries in the city alone. I saw most of the major ones including: Kunste Werk, Hamburger Bahnoff, Martin Gropius Bau, The Bauhaus Archive, Museum of World Cultures. I did not enter all but most of the good shows I saw.
Here is the Berlin Wall. It's the last remaining stretch still up. Beside it there is a musem setup by the German government called the Topography of Terror. This details the entire history of the Nazi Party up to and including the fall of Hitler and the Reich.
Next was Christoph Schlingenseif - really big player in German Art/Political movement. He has died a few years ago. At Kunste Werk they are now holding a giant retrospective of his work. He works mostly with Video and Installation pieces. Very extensive. Much of it I did not fully comprehend as it enters far into german cultural and socio-policial spheres.
Lastly I made a short trip to the Hamburger Bahnoff. This actually used to be an old train station, as it's name refers to. This is situated next to the newly (within the last 10 years) Hauptbahnoff, Berlin's central station. The museum houses lots of contemporary art, there was a big group show on when I went. Lots of Twombly and Beuys.
That's about all the museums I visited, quite a long post but thanks for looking!