I was in Berlin for 2009 for the 20th anniversary of the Berlin Wall falling. I stayed in an awesome boutique hotel in the former East Berlin called Abion Spreebogen, right off the River Spree. It's just off the Alt Moabit bus stop, and there's a beautiful small riverside park behind it with the part of the wall displayed as artwork and a sculpture garden.
I recommend visiting Checkpoint Charlie, where you'll also find a Berlin Wall (Mauer) museum and a fascinating line that divided the city in half. As mentioned above, the Potsdamer Platz is worth seeing, and nearby is the Reichstag museum (not to be missed). There the Kennedy Museum near the Brandenburg Gate, shopping at Aleksander Platz and you could even visit a concentration camp! It's Sachsenhausen, off the Oranienburg subway station. There are also nighttime shows, and cabaret which Berlin is famous for.
If you're looking to eat cheaply, all the Turkish-run sandwich shops are clean and the food is very good. Buy chicken doner mit salat (chicken sandwich with salad) for under $6 all over. You can even buy very good and inexpensive meals in some subway stations.
Have fun, guten tag.