it depends upon what your interests are, but I like the WWII and Cold War stuff in the city. Some of my favorites:

• DDR Museum - just across the river from museum island. Doesn't take that long to go through, but a great peek into communist East Germany
• The Berlin Wall - For me personally, I recommend the East Side Gallery. Some really great murals. The "My God, Help Me Survive this Deadly Love" mural is out there, and is iconic. An up close and personal look at Brezhnev's eyebrows. Haha.
• The Spy Museum at Potsdamer is really cool. Well thought out, with great flow and pretty fun. My son loved the bra gun. IIRC there was also a piece of the wall remaining at Postdamer Platz.
• Berliner Dom is great.
• Kaiser Wilhelm Memorial Church is really cool. It was bombed by the Allies in 1943, and the remains were left standing.
• The Stasi Museum is really cool, if not a bit eerie. Amazing just how much a government can spy on its people, and I think a poignant reminder.
• Brandenberg Gate and the Holocaust Memorial around the corner, across the street from the US Embassy. I was much more impressed walking through the columns here than that the Topography of Terror. I guess it's because it allows the visitor to be alone with their thoughts even though there might be numerous people walking through it.
• Reichstag Dome - Definitely get reservations for this. Commanding views of the city, including down to the holocaust museum, and you can also tell where the west and east parts of the city were. Don't miss some of the great documentation at the base of the dome - some real pieces of history here.
• Detlev-Rohwedder Haus - Now the German Ministry of Finance. Great piece of National Socialistic architecture which was commissioned by Herman Goring. There to make you feel small, and fit right into East Germany, post-WWII. Also has a piece of the wall across the street, and one of Berlin's most daring escapes was made by a family here, and there is also the Topography of Terror here.

Good, but not so much:

• Checkpoint Charlie - I guess you gotta go, it is iconic, and still cool. The Mauermuseum, has some really great artifacts in it; but it is really poorly presented and has no flow. Desperately in need of a good curator and a refresh. Even has a part about North Korea in there that, I guess, sorta makes sense?
• Topgraphy of Terror - Very sobering, but not a typical museum and not for bad weather. Some really like this one, but for me, it is down the list on Holocaust Museum/Memorials.
• Pergamon - I was unimpressed. Mostly because I don't care much for Islamic art and architecture, and the Pergamon Alter has been closed for almost 5 years and won't open until early 2020. After that, all you got is the Ishtar Gate, which is an oh well to me. Basically, without the Alter, give me the great museums of France and Italy any day. It just doesn't cut it.
• Memorial to the 1933 Book Burning at Bebelplatz - Just so so. Interesting, I guess, but not much else. The square and streets around it are beautiful, however.

Other than that, just take in the city. It has such a modern, youthful and vibrant feel to it. Much more dynamic than Rome, Paris and dare I say, even London. It is totally different than Munich, Frankfurt or Stuttgart. The food is great, and tons going on. Public transit is cheap, efficient and easy to get around. And if you are interested in the Cold War angle, I would recommend watching The Bridge of Spies before you go. And along with that, taking the opportunity to wander some of the former East Berlin apartment blocks, just to get a feel for the place.

Again, I loved Berlin, and can't wait to head back later this year!