First tip: start at the side of the Martin Gropius Bau. Because the outside temporary exhibition that became a permanent one, is chronological. It tells the story of the SS, that had its headquarters at this address during the nazi regime.
There is hardly anything left of the buildings. After (typically German) decades of discussion it was decided to leave the terrain as simple as possible. In 2010 a nice, minimalistic building with a theatre and exhibition space opened its doors. The information on display here is slightly less elaborate as outside, but (tip 2) it is less busy and comfortably warmer than outside.
In some way this exhibition about the nazi regime made a huge impression on me. At a certain point you almost become insensitive for all the misery in the history of Berlin. Topographie des Terrors still managed to touch me. A pity though that it has become such a major tourist attraction, leading to overcrowding: during the darker edges of day (tip 3) you have the best chance to be able to process all the information in relative quietness.