I loved the Reichstag, too. Also the river cruise, and an open top bus tour.
I went to the Alte National Galerie, because I wanted to see the Caspar David Friedrichs in particular, but I have also visited cities specifically to see galleries, because I'm into art like that. The MuseumInsel is worth wondering round anyway.
I found the Neue National Galerie quite moving, too, because they've got B&W photos of some works which were destroyed by the Nazis as degenerate. There are loads of other museums - I enjoyed the Bröhan-Museum, which has a lot of Art Nouveau and Art Deco (and was just round the corner from where I was staying. And the Bauhaus Museum.
The Historical Museum is good, too, because it covers a lot more than just the 20th century - I did a fair bit of 20th century German history at university, and you can have your fill of the Third Reich and East Germany, and it was good to find out more about the Prussian side of things. Though I did also do Checkpoint Charlie and the Wall and the DDR museum. Berlin was at the centre of so much 20th century European history.
I missed out on some of the other museums like the Currywurst Museum...
I also liked going up the Alexander Platz tower. Friends had a day trip to Potsdam, which they really enjoyed.
I think you need to work out what most interests you - there's no way you can do everything, so you need to pick and choose. Some of it is better only in good weather - I wouldn't bother with a river cruise if it's driving rain and grey and miserable. If you're not into museums and galleries, then there are things like the zoo and aquarium. There's also loads of shopping. If the weather's good, there's loads to see just walking round - we followed a couple of trails from the Rough Guide/Lonely Planet (whichever one it was we had.) You can also do stuff like Segway tours.