MUST do in Geramny:
Berlin: The city of artists is a MUST. You can party 24 hours a day and have everything imaginable available to you. Do one of those sightseeing tours to get a great overview. Some great things to look at beside the obvious Reichstag/Checkpoint Charlie and Brandenburg Gate: Funkturm, Citadelle in Spandau, Schloss Sanssouci, Schloss Charlottenburg and insider tip the Pergamon Museum! If you haven't seen Berlin, you have NOT seen Germany.... oh - Bonus spot just south of Berlin - Spreewald! Imagine going around by boat like in Venice everywhere....
Hamburg: Reeperbahn (red light district), Fischmarkt and the biggest Container Harbor in the world (if memory serves me right)
Luebeck: Totally agree with Luebeck... Very historic city
If you love really old building and history: Heidelberg and Rothenburg an der Tauber!
Cologne is cool but take a look at Koblenz!!!! Do a tour on the Rhine looking and all the castles along the river and visit the Castle Ehrenbreitstein in Koblenz.
Munich is a must as well as Nuernberg... Then you have the black forrest etc.. Totally agree with Berchtesgarden. When in Austria may I suggest Seefeld, Tirol?
Also, if you do some of those cities already... think about Brussels (hate the people LOVE the city, museums and buildings), Amsterdam and Prague!!!! WELL, worth the time spend there. When in Austria take a short trip down to Milan or hit northern Italy.
Oh man.... I need to travel some more and see those places again....