Can I also recommend a walking tour?
I used these guys a while ago and they were great:
http://www.insidertour.com/
The tours are led (well, they were when i did it

) by Berliners who lived in Berlin during the fall of the wall - and the stories they tell as they take you around the city are amazing.
It's a full day affair - the tour actually went an hour and a half longer than the stated time. Took in the whole central area... zoo, gardens, parliament, wall, museums, Brandenburg gate etc etc.