I think that with 3 days in each city you'll be fine - I would add a day to Berlin and delete one from Budapest - just from my experience of seeing those towns several times. And it takes a day about to go between each - on the way to Prague consider stopping off for a few hours to have a look at Dresden, one of the most amazing and interesting cities in Europe - the so-called Florence on Elbe - throw you bags in a train station locker and walk to the Elbe, the riverfront where most everything of interest is located.

For just being in cities cars are rather useless - expensive to park and in places like Prague subject to break-in (occasionally but a possible according to reports) - city transit systems are so so good - buy a family pass for a day or more in Berlin - this will even take you all the way out to Potsdam, and the stellar Sans Soucci Palace, Frederick I's Prussian Versailles - sweet park also.

For lots on trains in this area I always spotlight these IMO fantastic sites - www.seat61.com (good info on online discounted tickets that are much cheaper often than full fare just show up and buy tickets; www.budgeteuropetravel.com and www.ricksteves.com.

Forget about any railpasses - you are not traveling enough - use www.bahn.de/en for schedules to Dresden and Prague and advance discount tickets that are easy to do on this site - note those tickets are non-changeable and non-refundable so be sure of your times. Put in Berlin Hauptbhanhof for your start (or other Berlin station if that is more convenient to your hotel.

Don't know much about Prague to Budapest but may have discounted tickets as well but trains in those countries are still quite cheap compared to full-fare in Germany at least.

Paris, Amsterdam and Munich would work equally well but are much more expensive overall - Eastern Europe is also IME still more old-fashioned - except Berlin - and not as many folk speak English, etc.

Great choices of countries, I am sure you will not be disappointed. Train is the way to go in europe, they are convenient and drop you at the city centre. I strongly agreed with PalenQ, that you don't really need a train pass as your travel date is in september, you have plenty of time to book discounted ticket. Have you started looking at flights? ideally you will want to fly open-jaw so as to minimise time wasted on traveling.

I did Prague, Vienna and Budapest 2 years ago and it was easy traveling between them. You might want to consider this option as well and decide which countries interest you the most!
http://www.fodors.com/community/europe/prague-cesky-krumlov-vienna-budapest-trip-report.cfm

Thank you both so much - you guys were so helpful!

Some people I've seen recommend Paris, Amsterdam or Munich in stead of Berlin>

Well those are certainly logically paired cities and the travel time between them is about the same as the three farther east. In this case I'd fly into either - whatever is cheapest and do an open-jaw and fly out of the last city on your trip - again the cheapest combo.

Say start in Paris - 3-days
Amsterdam 3 days
and Munich 3 days - with one day trip say to Neuschwanstein Castle or just out to Dachau Camp. I couldn't say which three city groups would be better - you can't go wrong.

Berlin, Prague and Budapest
Paris, Amsterdam or Munich instead of Berlin

There's no right or wrong itinerary... just depends where you want to go! Any 2-3 of those cities could work just fine.

Those cities are all great - but 9 days is really only enough time to see 2 of them. If you try to do all 3 you will spend 1/3 of your time on the ground getting from one place to another - and have only 2 days in each city. Possible but you will end up missing a lot.

You will end up "missing a lot" regardless. You could spend all 9 days in any one city and hardly scratch the surface.

You will end up "missing a lot" regardless. You could spend all 9 days in any one city and hardly scratch the surface.>

IMO you will end up missing a lot if you stick to one city for the whole nine days - you'd miss two other great cities. IMO nine days in any place would be boring for the average tourist. I just cannot imagine what I would do with nine days in Prague or nine days in Budapest!

PalenQ - I agree, for me atleast - sticking to one place for 9 days will get boring and with only 9 days I do miss a lot at the same time jumping between 3 cities because there usually is so much to see in these cities but I gather have 2 days in each city than none because who knows when the next time I can visit will be. I only spent 1 day in Rome - while it did not scratch the surface, I get to see everything I wanted to with the time given.

After looking into some places, I def. want to be able to see the Neuschwanstein Castle. I chose Berlin over Munich solely based on the opinions of various friends who have visited both. I'm going at the end of September during Oktoberfest, where Munich obviously host the main events - I did hear Berlin has its own little "Oktoberfest"

Shareen AND what you see in between those cities is the Europe that lay between them - like when going between Berlin to Prague (know you changed to Munich) the train rolls right thru gorgeous Saxon Switzerland, hugging the Elbe River the whole way thru one of Europe's very prettiest river gorges.

In Czech Republic you see the landscapes too as well as rotting industrial detritus from commie days when heave industry trumped all.

I think Oktoberfest was great - each of the several times I went! Though all German towns seem to have Octoberfests none can match the Bacchanalian festivities at the one at Munich!

Munich vs Berlin?

wow tough choice - if you eliminate Budapest you could do say Munich, Berlin and Prague

or Amsterdam, Berlin and Munich

Berlin is so fascinating to me right now - a world capital city being rebuilt right before our eyes - well largely done by now but still a work in progress - Munich has never excited me too much as a city but more for the day trips it presents, like to Neuschwanstein or Dachau.

If doing Munich to Prague note that direct buses are better than trains, taking an hour less.

"I just cannot imagine what I would do with nine days in Prague or nine days in Budapest!"

Sounds like you didn't care for Budapest. I, on the other hand, have visited three times and would be happy to go back. (You can click on my name for a couple of TRs including Budapest.) But I found Prague overcrowded and haven't been back. Since we don't how the OP will react, it makes more sense to split the time equally.

No it is not that I did not like Buda or Pest - I did - just that perhaps given the OP's wish for Munich OP could substitute that for Budapest and reduce travel time and distance as well. I will say that nine days in Buda and or Pest is a bit too much but I do agree that those are fascinating cities - OK I admit I found the smog in Budapest a big overwhelming and that may have colored my take a bit.

But Budapest is a fine city - no doubt about that.

I didn't notice any smog - when were you there? I think the air is a lot clearer in Eastern Europe than it used to be as the Soviet era factories have closed down.

Ok to be fair it was several years ago and Paris has notorious smog too and it does not ruin it - yes things in Eastern Europe change quickly - thanks for the upbraid!

Thanks for all the feedback - it's been very helpful!

Do any of you have any opinions on getting from Budapest-Prague and then Prague-Budapest? I am inbetween flying and/or train.

It's a long train ride during the day and there is also an overnight train between them - sleep on the train unless you are the type that cannot - most can and I never have had a problem in zillions of night trains - save on the cost of a hotel as well.

That night train is about 3 hours longer than the day train. Try to fly.

Actually about two hours longer but I do not see the point - the efficacy of an overnight train is you can sleep and arrive in the city center about 8am in the morning and also save a night in a hotel. One problem though is that it does not leave Prague till about midnight - sometimes the train will be standing there well before that for boarding however - however I do not know if this is the case.