We are a family of 5 that will be flying into Prague for a few days and then we plan on driving to Salzburg. We want to have a car in Salzburg because there are many day trips we would like to do.
Can anyone give us advice on where to rent a car in Prague and then where to return it in Salzburg?

Can't help with you primary question but just so you know, renting a car in country A and returning it to country B normally entails an enormous extra fee. Someone has to drive the car back to country A.

Yes take the train to Austria then rent you car for reasons StCirq gives. Czech the Czech Railways official website for the best fares. for info on trains: www.seat61.com- great info on how to book your own tickets at the cheapest price;www.ricksteves.com and www.budgeteuropetravel.com.

Is Vienna in your plans - if so the train trip from Prague there is shorter than to Salzburg and pick up your car there.

Just wanted to add that, having recently ridden on a Czech train running between Budapest and Brno (we stopped at Bratislava), I was blown away by what a great railway it was. Really state-of-the-art. The guy making food in the bar car was wearing a toque! OK, maybe an affectation, but the whole experience was a far cry above the SNCF, which I am very fond of.

Czech mainline trains are up to snuff with western Europe but some of the sidelines are not.

I can believe that.

Thanks for your replies.. we do have plans to go to Vienna after Salzburg, but perhaps we will go from Prague to Vienna by train and then rent a car in Vienna and drive to Salzburg?
Does that sound more logical? We wanted to take a trip to Cesky Krumlov though, so we thought that we could do that on the drive to Salzburg.. so many decisions!

You can take a train from Prague to Cesky Krumlov. However the train trip from Ceske Krumlov to Vienna is not as easy. I slept in Ceske Budejovice instead of Ceske Krumlov, as it has better train connections, and recommend doing the same. It also has an excellent central square.

For schedules see bahn.de

Is there somewhere you want to stop between Vienna and Salzburg?

Prague to Vienna by train and then rent a car in Vienna and drive to Salzburg?
Does that sound more logical?>

Yes and you can with an Austrian rental car dip up into Czech republic if you want to see C-K en route to Salzburg- good really only if you want to spend the night there probably or a long day trip.