14 Days in Europe - Salzburg and...? Help!

I would get the plane ticket first and then drill down and fill in the blanks
Something like
Fly into Prague 4
Cesky Krumlov 2
Salzburg 4
Fly out of Budapest 4
or vice versa
You might get a guide book to stay organized with the responses you'll get here

It sounds as if you're game to live a little of the Bohemian life, and you picked some of the premier lively cities to visit.
I'd suggest flying into Budapest--our favorite "new" city. (We'll be back there next month.)
Then take a train to Vienna--another great large European city whose nightlife is understated. (Stay at K&T Boardinghouse.)
Then take the train to Prague and stay in the central city. We took the "Free Walking Tour" and went back the first night for their "Nightlife Tour" to learn where the really great bars and restaurants are.
There are a number of shuttle companies operating out of Cesky Krumlov that will pick you up in Prague and take you to C/K. Then, they'll take you to Salzburg.
It's a 2 hr. max train ride from Salzburg to Munich--a great place to fly out of.

I personally would skip C/K and Prague and go Vienna-Salzburg-Munich via trains. You might have time to rent a car and head south into Tirol and the Austrian Alps around Innsbruck. (Prague is somewhat like a more expensive Budapest.)

Hi David, thanks for the reply. A couple of follow-up comments...

1. I forgot to mention that Oktoberfest in Munich begins on Sep 16. The general opinion I've gathered is to avoid Oktoberfest - massive amounts of people, cost of everything goes up, and that it is overrated in general. Since we're leaving Europe on Sep 19, we were trying to avoid flying out of Munich. Would you agree?
2. Do you think Vienna fits our interests? I've been reading other threads and seems Vienna is often recommended to folks who really enjoy art and museums and want to spend their time in the big city. If we went with an itinerary like Jazz+Travels suggested, would we be completely remiss to skip Vienna?

Vienna has lots of history and lots of beautiful architecture (and not all of it is Hapsburg baroque!) There are crowds at 'ground zero' locations, but it is easy to bypass much of that. We have neighborhoods, local places, etc. We also have lots of booze and food.

But Jazz's list looks fine to me. It's your trip and your interests come first. :-) Be aware the krumlov and prague are in the middle of the beaten path nowadays.

For hiking: Southwest of Salzburg, the Dachstein/Schladming area is great. You can take a bus from Schladming train station, up the valley and go up the Alpinsteig through a waterfall canyon (ladders, hanging bridges, etc) and come out at a lovely little valley with a lake. There are plenty of multi-day routes, but you can do this one in a day.

A nice little interactive map of the area. The H's are bus stops. Click on a route to get details.
http://www.wildewasser.at/de/wasserwege/index.php

Your primary interest is "Food, beer and wine", and you're skipping Oktoberfest? Its a world-class event - so what if there are crowds! I thought it was over-rated too, before I saw for myself. Kind of like saying Mardi Gras in New Orleans is not worth seeing once in your life.

You might consider dropping one of the well-known destinations for a second Hungarian town. I've only been to Budapest (briefly, 45 years ago!) so can't give you a personal recommendation, but our poster James E travels to Hungary often and I know he has offered some suggestions outside the capital city in earlier threads. I think you'd find any Hungarian town/city other than Budapest much, much less touristy than your other destinations. (Well, maybe excluding Sopron where people go for inexpensive dental work.)

Your primary interest is "Food, beer and wine",

Then you should experience Vienna in this three categories.