The Topography of Terror museum in Berlin is on the former site of Gestapo HQ. It was a damn disturbing look at the culpability of the German people, and I recommend it. I also took my children to the Berlin Wall memorial. Also worth the time.
I took a Viking Berlin-Prague river trip in May but American Airlines cancelled 2 consecutive flights and delayed the third 4 hours, all I got to do in Berlin was sleep one night in the hotel and board the boat. Bummer.
Both are on our list for our Germany trip a year from now. We arrive in Munich where we will be for 4 days, with side trips to Dachau and Nuremberg from there. Black Forest area for 2 days with a day in Cologne before heading to Berlin for 3 days. WWII stuff should be well represented with this trip.