20days Germany - Prague - Austria - Swiss - Paris - Amsterdam

You say you traveling in mid-September, if it is at all possible try and postpone your tip until the first week in October. Mid-September is still considered high-season in Europe, and costs will be much lower two weeks later; so will the crowds.
In terms of the itinerary I would thin-it out a bit and eliminate Innsbruck/Munich, and spend the extra time in Paris and Amsterdam.

You can't "cover all the main attractions" in Germany, Czech Republic, Austria, Switzerland, France & the Netherlands in 20 days. Especially if you spend nine of those days on the train.

You can have a memorable trip--so I'd work on that rather than on bagging all the sights. Good luck!

I've decided to change my route. I would like to go to Germany, Czech Republic, Austria and Switzerland. Now that I have an additional 4 days, which place do you think I should spend more time on?

I would be travelling from city to city by train and bus. My first destination would be Berlin and last destination is Zurich.

I was wondering if it's possible for me to cover Neuwanstein Castle and the Romantic Road.. I'm not sure if it's on the way or near to one place or another.. If it's totally not possible and out of the way, I would like to skip this area.

The reason why I chose Munich was because I would like to experience the Oktoberfest and since I'm there, I would like to visit the place.

I haven't decided which part of Switzerland I would like to travel. I was thinking of Bernese Oberland and maybe at Lucern a day or something. I was thinking of something scenic for both Austria and Swiss. I was thinking more of a 'Sound of Music Tour'.

How long is it to travel from one city to another? I would be travelling in the following sequence.

Potsdam to Prague, Prague to Vienna, Vienna to Salburg, Salzburg to Munich, Munich to Innsbruck, Insbruck to Lucern.

I flew into Berlin and out of Zurich. (My itinerary included 3 weeks in Germany, Austria, and Switzerland). I would save Switzerland for last. I went non-stop through Germany and Austria...then relaxed in the Alps before leaving. It worked out quite well because I could enjoy some lazy hiking and unwind before heading home. Just keep in mind that Switzerland is VERY expensive. I am a student too and I liked having an agressive schedule. If I'm traveling, I feel like I have to be doing something all the time. If you get restless easily, I would skip Salzburg. I thought I had to go for the Sound of Music Tour, but I thought it was overrated. It is fun walking through the gardens - which are beautiful - but it wasn't worth it for me. I watched the Sound of Music Special Features on DVD and the woman on the bus repeated almost exactly all the information again. Everybody just likes different things and that's just my take. :)

You can visit Innsbruck and Salzburg as day trips from Munich on the Gayern Ticket, which allows travel thru out Bavaria- parts of Switz and Austria, too, for €27.
Potsdam is also a day trip from Berlin. You should probably cut out visiting one of the cities as you will spend most of your time travelling and checking in.
Paris is so cool that we would advise spending a day more there and less time in Switz.