Depends what you like, really - I could go on for hours!
The bus tour isn't a bad way to get an idea of how the city is laid out, especially going across East and West. Apart from all the museums on Museum Island (love them all, but you may have to book ahead for the Neues Museum) I would always recommend the Jewish memorial (the exhibition underneath is wonderful, but harrowing), and the Jewish museum itself is good. Brandenburg Gate/Potsdamer Platz are very close to each other, and there's the big Sony Centre at P. Platz. Checkpoint Charlie - the museum there is also excellent.
Head to the Kurfurstendamm (former centre of West Berlin) with the bombed out memorial church and the KaDeWe (giant department store with amazing food stall). The KuDamm is a pretty good shopping street.
Food/drink-wise - Hackescher Markt (just behind the S-Bahn station, near Alexanderplatz) has a number of bars/restaurants. Brauhaus Lemke is a place there that we keep going back to. Oranienburger Str/Friedrichstrasse have loads of bars/restaurants (I like Oranium, near the synagogue). Tacheles on Friedrichstr is a former government building that was taken over as a squat and now houses an artists collective and a few bars ranging from funky to downright grotty, but there are loads of more 'normal' bars around there too. Head for Prenzlauerberg in Mitte if you want something funkier, or Simon-Dach Strasse near Warschauer Str station has lots of great bars too.
Other good tours include various cycling tours (it's a really flat city and great for cycling), or there's the Trabi Safari, where you get to drive a brightly painted Trabant in convoy around the city, with guides pointing things out to you (brilliant fun).
Let me know if you want any more info. Public transport is great, it's really easy to walk around, and you'll have to have a currywurst from one of the stalls! I'm really envious (can you tell?) - will have to plan a trip back soon.