The number 100 public bus is a good option for travelling along the main west-east spine of the city
http://www.visitberlin.de/en/article/experience-berlin-by-bus-100
Checkpoint Charlie Museum
The bust of Nefertiti in the main museum is surrounded constantly 10 deep by tour groups, so get there very early or very late if you want to get closer
The Pergamon Altar and the Ishtar Gate are awesome
IMO the Fernsehturm is over-rated as an experience, long queue to go up a tall tower ho hum.
Splendid natural history and archaeology museums
It all depends on what you want to do -
http://www.visitberlin.de