You've already got some good suggestions.
If you're into museums, museum island is the place to be - Pergamon, Neues and others. Do some advance planning for tickets. We waited in line for a ridiculous amount of time to get that sorted out. Nearby is the Berliner Dom - get up onto the roof for a good view. Get into the basement for a crypt tour.
If you're a foodie or a shopper, KaDeWe is a well known store. Find the food bar/counter with rosti and Kostrizter Schwarzbier - yum!
Memorial - mother with her dead son sculpture in the Neue Wache on Unter den Linden. Easy to stop in as you walk by. Near museum island. The walk from the Brandenburg Gate down Unter den Linden is worth the time by itself.
Memorial to the Murdered Jews of Europe - within walking distance from Checkpoint Charlie and Brandenburg Gate. Was more moving in person than it looked from pictures. Of course, we also went first thing in the morning, so we were the only ones there. Hilter's bunker location is pretty close and is marked with a sign. It is a parking lot, so nothing to see.
Brandenburg Gate - obviously. However, go very early or late to get the place to yourself. Very different vibe with tourists buzzing around.
East Side Gallery - need a train ride to get there, but a famous part of the wall that has been retained and painted by artists.
There are lots of other things to see, places to go, etc. Presuming you're looking for the high points from a tourist perspective and want to stay in the city.
