I visited Hamburg from Berlin , really liked it.
I don't care for small towns, so my vote is for Berlin
( been four times) and Hamburg.

My two cents:

I lived in Berlin for 3 years and would go back there in a minute. So much to see and do there, especially if you include Potsdam. I think you could easily fill your 4 days in Berlin/Potsdam, but if you really want to take a day trip from there, Dresden and Leipzig are each about 2 hours away by train. If you are visiting in the summer, Luebbenau (in the Spreewald) is a nice day trip as well.

I think you have seen some of the best of Bavaria already, so I'm not sure I'd recommend a return visit just to see Bamberg, Regensberg and Nuremberg.

Hamburg held no interest at all for me.

I am a big fan of getting to know all the regions of Germany. It's so diverse - you will find Berlin to be so very different to Bavaria almost as though it were a different country. Combine Berlin with a tour of the Baltic coastal cities, or a trip through the Spreewald as longhorn advises, or maybe take in the townships of the Harz Mountains (Goslar, Quedlinburg).

Lavandula

Berlin: http://www.flickr.com/photos/mksfca/sets/72157623174831107/show/

Thanks for the quick reply. I will take a look at some of the suggested side trips around Berlin. I am torn because I have been to Berlin before, and thought perhaps Hamburg deserved some time. However, my research shows considerably more to do in Berlin.

We plan to be there 2nd week of October.

I like the smaller towns. Bamberg is lovely, as are Regensburg and Nuremberg. It depends on what you like to do, of course. But all three of these are great for just strolling around, soaking in atmosphere.

Hamburg is quite OK in my book - I thought it was an interesting enough experience, with a tour of the harbour (which is a working harbour), but the architecture is not a big drawcard, so you essentially have just a big city experience. I got a lot out of my visits, particularly my first (over 20 yrs ago), because I was learning German at the time and I had fun with the local dialect, and the local dress habits of the older men, who all wore fishermen's caps. Also you will find herring and smoked eel as snacks at the train station. So there is still quite a bit to be fascinated with, especially if you want to contrast with Munich or indeed Berlin.

The Hamburger Dom (the funfair) is quite a lot of fun. Elegant living - the inhabitants are prosperous and there are lots of good restaurants. hsv, who used to post here, has been a contributor on several good threads about Hamburg restaurants, so do a search. And if you are fascinated by red light districts or nightspots there is the Reeperbahn / Große Freiheit. I live near a red light district in my own city so I find this less fascinating.

You might productively combine Hamburg with a trip to Bremen and Lübeck. Lübeck in particular is different, like the Baltic cities it has the brick gothic architectural style and is really worth a stop, and I like Bremen too for its medieval Rathaus and the Schnoor district.

Lavandula

Berlin is the place to be... you always find something to do there and every corner has something interesting !