Vienna is expensive. €20 for a schnitzel. You can pay less but you are struggling to find a table.
Prague is mostly a tourist trap unless you decide in advance where you want to go and use a map.
You need to do the same in Berlin but for a different reason: the place is vast and you can wander around for hours looking for something. The former East Berlin at Mitte is where everything of interest is.
I agree with Steve. Avoid Northern France in late September. Head South or East, preferably East as late September can be stormy and wet in the South of France, certainly near the Mediterranean.
Central France is generally ok but there isn't much there in terms of cities with enough to do apart from Bordeaux and Lyon. France is generally expensive anyway in larger cities.
I'd recommend the following:
Munich. Make sure that you take in the concentration camp at Dachau. Everbody should visit one in their lifetime. Other points of interest are the Olympic village and the tower that looks out as far as the Alps. The BMW museum, showroom and plant is nearby too and is worth a visit. For beer go to The Augustiner Keller, the Hofbräuhaus and the little Kloster Andechs pub in the middle of town. Despite its appearance (it looks touristy) this are is frequented by locals who are very friendly. Munich is as big as Vienna, not quite as grand and without the swagger but is decidedly cheaper. The beer is also better. Excellent public transport.
Saarbrücken is quite charming and a tram will take you over the border to France. I mention it because it is reachable by train from Munich within a few hours.
Ditto Heidelberg.
Bratislava, 40 miles from Vienna. Beautiful in the Old Town, a little run-down in parts but it has its charms. There are also great places to eat and drink but all are outside the Old Town. Dirt cheap.
Brno, the Czech Republic's second city. Great food and beer and dirt cheap. The public transport is also good within the city and for travelling to other places like Olomouc or even Bratislava.
Ljubljana, the capital of Slovenia. It's perhaps a bit far but worth a mention. We went there in July and enjoyed it so much that we're going back in mid-september for 5 days. A beautiful city with stunning scenery. You can also see the Julian Alps bordering with Austria without climbing a tower! Food and drink are good and very reasonably-priced. Think German, East European and Italian fusion! The locals are exceptionally friendly, as we found. The trains are virtually non-existent but the buses will get you out of the city to other places of interest in and near the Alps like Lake Bled and Kamnik. The best way to get around within the city (it isn't that big anyway) is on foot or by bicycle. You can hire municipal bicycles for peanuts.
http://www.seat61.com/international-trains/trains-from-Frankfurt.htm#.Vc8VcXhwbqA