Which Eastern European cities are better in Sept?

If when you say you have 2 weeks, you mean you literally have 14 nights on the ground in Europe then I think you need to cut out two places, at the very least. The ones you cut depend on your specific interests and your travel history. Definitely fly into your first city and home from your last to save backtracking time.

Prague, Krakow and Berlin come to mind as 3 good stops but Krakow is hard to get to from a lot of cities, transfer-wise. Berlin, Prague and and Vienna wouldn't be bad on the train. If you choose 3 cities and allocate 3 or 4 days to each, you could add a fourth city that is in between two of the others, making for a nice 2 night stop in a smaller city you might not otherwise see. You could do Berlin, Prague, Vienna and then spend a couple of nights in Salzburg and fly home from there. You've got a lot of options but you need to do a little research to pare them down.

When you say you are going in September, do you mean September of this year??

Thanks for the tip. Yes, arriving Europe on Sept 7 in Berlin and leaving Sept 19 from Vienna. Interested in mountain scenery, medieval castles, visiting different cultures and new eating experiences. Although weather is unpredictable, places where it is more apt to be sunny. Also, places not jammed with crowds. Plan to stay at hostels. Reason Krawcow is on list is due to Polish heritage.

If you weren't flying into Berlin I'd suggest shelving it for another trip because there's so much to see there. As it is, I guess maybe Halle (which I haven't seen) and Ljubljana (which I like a lot) are a bit out-of-the-way and could be targets for omission. But the remaining 5 cities would be a lot to cover in 2 weeks. Traveling from place to place is going to take large chunks out of 4 of those days.

I was planning an almost identical itinerary for 2017 except I included Budapest and I have 32 days. Since I want 8 nights just in Vienna I had to split up the others over the remaining three weeks. It really wasn't workable unless I wanted a couple of stops if only two days.

I think you need to eliminate one city in the very least, two would be better. I would look at your outliers; Berlin, Llubjana, Cracow.
Going along with Valerie, the transfer to Cracow has become the most difficult part of my planning. Looks like I will be bussing it there from Prague instead of taking a train. I decided to eliminate Berlin and will do that on a future Germany only trip.

So my planned travel route is Prague, Cracow, Budapest, Vienna, Slovenia (sleeping in Lake Bled and taking the public bus to Llubjana) then St Gilgen/Salzburg. There is a public bus running fromSt Gilgen to Halle so that will be a day trip.

Assuming you haven't booked your air yet, do a multi city flight. My last stop is St Gilgen/Salzburg. I found better fares flying out of Munich vs. Salzburg. Also Munich to Charlotte is nonstop and I really like that aspect. There are daily shuttles from Salzburg direct to the Munich airport, very reasonable, so I will spend my last days in Salzburg area and take the 0700 shuttle to Munich for my noon flight home.

Good luck with your planning. It's really hard when you have to cut a destination.

Planes are already booked, correct?

You could follow a fairly logical, linear path Berlin---Prague---Munich (transfer to Salzburg)---Ljubljana---Vienna. The first two trips involve 3-4 train hours ( or maybe bus from Prague to Munich) and the last two are more like 5-6. But if you want to to include mountains you should keep Salzburg and Ljubljana ( or get off the train at Lake Bled, since it stops at Lesce Bled before going to Ljubljana). But the bus from Munich to Ljubljana is faster than the train.

Logistically the easiest would be: Berlin (you land there), Prague, Vienna (you fly from there). On the way from Berlin to Prague you can stop in Dresden, from Prague to Vienna in Brno. There are no magnificent mountains on your way only nice wooded hills and several tunnels on the part of way between Prague and Brno. For the mountains you would have to go to Salzburg or Ljubljana but with only two weeks I don't know - probably too much hassle. Rick Steves recommends 3 castles around Prague. Out of those three Karlstejn is the most picturesque and easiest to get to. I don't think you would have time for more. Maybe Spilberk if you stop in Brno. It's on the hill practically in the center of the city.

Berlin >> Halle >> Salzburg >> Vienna
Or
Berlin >> Prague >> Vienna

Since you really only have 12 nights on the ground I would say drop Krakow, Ljubljana, and Halle and do Salzburg as a day trip from Vienna - 4 nights Berlin, 3 nights Prague, 5 nights Vienna with a day trip to Salzburg.

Thanks for the tips everyone!!! I think I will cut my stay in Berlin short. I think Austria will be saved for another trip. So Berlin, Prague, and Vienna.

You have two full weeks. If you are working on a music theme, then I would say three cities to be visited...Halle, Salzburg and Vienna. If not, Krakow can be done if you want to a take night bus and night train from Krakow. Stay longer if Berlin so that you see Halle as a day trip. I did that in 2015. For the "whirlwind train trip" I suggest Berlin (with Halle), Vienna (with Brno), and Salzburg.

I'll be in Berlin at the same time, so I certainly hope it's a good time to be there :-D

I've been to Berlin and Prague in early October before, and the weather was beautiful, if a bit on the chilly side.

I'd probably start in Berlin then Prague, Vienna and end in Ljubljana (or maybe see Trieste or Venice for a flight home option). Berlin and Vienna have a lot of must sees. You could spend two weeks on the two of them (maybe with Dresden and Potsdam as intermediate stops).

I love Salzburg. Krakow is high on my list of places to see. Both are out of the way to the itinerary I mentioned. You would have to make one or the other a key part of the trip and skip other cities. I think Salzburg is a natural with Munich and Vienna is a natural as part of a more eastern (really central European) swing. Krakow might be best as part of a loop through Poland.

The top of my list in this group is Vienna. Berlin and Prague are probably the top of most people's lists.