I usually try to have some sense of where I am going by reading guidebooks before establishing an itinerary. In your case, I suspect that Prague is too short, and Munich would be if only a two night stay.

As for the train part these sites will help a lot IMO - www.seat61.com; www.budgeteuropetravel.com and www.ricksteves.com.

You may look into a Eurail Select Saverpass for Switzerland, Austria, the Czech Republic and Germany if you want first class travel and there are IME of decades of rail treavel in Europe significant differences in class - much more relaxed in many ways though many find 2nd class perfectly adequate - but if first class the pass may save you money and let you hop on any train in all those countries practically - just show up - for 2nd class try to score deep discounted tickets online - those however are sold in limited numbers and must be booked months in advance often to secure and are generally non-changeable nor refundable.
Potsdam can be reached by S-Bahn train from anyplace in Berlin - in cities like that investigate day passes where several folks can travel unlimited times for a pittance.

Geneva to Munich - via a change of trains in Zurich - a long day of 6-7 hours I would think.

Munich to Prague is a long day if by train but if you take a train to Nurnberg, just north of Munich, there are several daily buses to go to Prague and probably constitute the quickest route all told (if railpass it is valid also on the bus, normal fare about 50 euros - discounted limited in number fares about 19 euros.)

Note that there is also an overnight train between Munich and Prague I believe - save travel time in not so exhilarating scenery and the cost of a night in a hotel as well. Bargain rates can be had at www.bahn.de/en - German Railways web site.

As the train ride Prague to Berlin is now fairly short you could break your journey in Dresden and spend a few hours traipsing around that historic Florence on the Elbe - put bags in station locker - lots of trains to reboard - but if you get a discounted Prague to Berlin ticket I do not think you can break your journey on those restricted tickets.

IMO consider staying a night in Dresden if possible.

Thank you so much PalenQ for your suggestions! They are much appreciated.

Kcfoonian - thanx for the thanks!

Actually, there is now a direct bus between Munich and Prague, so no need to take the train to Nuremburg and change to the bus there. The trip takes 5 hours and if you reserve your tickets ahead, can be as low as 29 euro/person.

The direct train takes 5 hours and 50 minutes.

For overnight trains - it looks like the service between Munich and Prague was discontinued.

Yes thanks nov moon for the info on the overnight train Munich to Prague being scrubbed - I can see no mention of it in schedules though sometimes in summer they may run such trains at times.

Buses according to www.bahn.de take 4 h 39 minutes so are more than an hour faster than the direct train - and these buses also honor railpasses for the basic fare - not the mandatory see reservation- a few euros I think.

LOVED Mike's Bike tour in Munich, also toured Dachau (history major) -

took the train from Prague to Munich and back - train changes were a pain