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munich
Go to Jagdschlössl at U Rotkreuzplatz for proper bavarian food.
http://www.jagdschloessl-muenchen.de
Definately recommend their "Münchner Tellerfleisch" and "Ofenfrischer Braten von der Sau"dusseldof
..avoid "Alt" beer!
berlin
..like somebody said, there's a lot of great food in Berlin. There's also a lot of shit food in Berlin though.
Would help to know where you are and what you're after.
There are traditional / regional dishes in Berlin as well, but compared to bavaria it's basically all shit.
think munich, dusseldof, berlin, and maybe one other...