I am considering a multi-city trip in October 2012 to Berlin, Munich, Vienna, Salzburg & Prague. Thought of starting in Berlin but having read about the indefinite delays to the new Brandenburg Airport that was scheduled to open next month, which airports in the cities mentioned above would be best to fly into?
Both current airports (Schonefeld and Texel) are relatively easy to access from the central area, though Texel requires buses instead of trains and buses, on my books, are inherently crap.
While Andre L. has a problem with buses from Tegel, I did not. But, Tegel is close to the centers of Berlin (east and west), so a taxi is not unreasonable (that's what I did for three of my four journeys there and back). Between Tegel and Schoenefeld, choose whichever has the best fare, most convenient connections, etc. For your other cities:
Prague only has one airport. Vienna has its own airport, but budget flights sometimes fly into Bratislava in Slovakia and call this "Vienna." It's over an hour away; Rick Steves books have the details about options from getting to Bratislava airport to Vienna. While Salzburg has an airport, Munich is only two hours away, and MUC is a much larger and busier airport. I'm assuming you're flying into one of these places, taking trains between the others, and then flying out of the last one (flying "multi-city" or "open jaw" to avoid backtracking). If you're not, you should be. I went right from Vienna to Berlin, so I flew, but with all the cities you want to see in between, flying between them makes no sense.
The TXL bus from Tegel to Hauptbahnhof and Alexanderplatz is excellent, reliable, easy to use... for all of us but the people who we make drive with yellow license plates to other motorists can spot them from far. So just don't worry about it. Lufthansa (and partners) and Air Berlin (and partners) will continue to fly in and out of Tegel (TXL) until the new airport eventually opens. Most other airlines fly in and out of Schönefeld (SXF) and there is an easy train service to and from the city's center. Munich only has one airport (unless you fly Ryanair, then it has two but the other one is 100 miles from Munich). Vienna only has one airport (even Ryanair calls the other one Bratislava). Salzburg only has one airport AND there is a bus service from Munich airport to Salzburg. Munich to Salzburg actually is a train ride. Prague has only one airport but from Berlin to Prague vv. you would actually take the train as well.