Definitely Berlin! Hamburg probably for one day to see the famous red-light district and in case you want to see the something "typical" german in Bavaria I would recommend to choose Nürnberg over München. For a really nice nature experience check Lake of constance absolutely beautiful and you can be in Austria, Switzerland and Germany in one day. about 8 years ago
There are so many. In Bavaria there is Munich, the castles of Chiemsee (on an island in a lake on the way to Salzburg), Linderhof and fairytale Neuschwanstein (near Fussen) on the Romantic Road route which ends in Wurzburg on the other side. You can catch the bus from Munich, it heads south first to Neuschwanstein & then north through some beautiful villages, the most famous being Rothenburg ob der Tauber. Berchesgarten with Hitlers Eagle Nest is a must do for history lovers. Friedrichshafen on Lake Constance & the home of the Zeppelin is well worth doing it, from there you can do a trip by boat into Switzerlands Rheinfalls or to the other side of the lake where there is Austria & the Alps. You can take a trip in the Zeppelin but its expensive & subject to weather disruptions.
Bonn is great particularly if there's traditional music going on and the medieval town of Bad Munstereiffel in the Eiffel holls is worth visiting from it.
The university town of Heidelberg is worth a visit, the walled city of Nurenburg is amazing & a must for history buffs & Berlin is fantastic. A trip up the Rhine by the Lorelei is worth doing. about 8 years ago