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Exactly how many days will have on the ground? Exclude your arrival and departure days from the total. And think in terms of nights. For example, 4 nights in a city equals to 3 days of sightseeing.

Please provide your interests (history? Art? Food?) In order for us to provide suggestions.

Regardless, doing some basic research in the region will help at least for a base idea of where to go and for how long. In each city/location identify your top priorities for sightseeing, which will give you an idea how long you need. Figure time at most museums and historical landmarks (castles) to be roughly 3-4 hours, depending your interests.1-2 hours for smaller sights (i.e. some churches, small museums). Again, time of year is a factor - especially in Prague. August is VERY busy.

Figure your time in transit, plus checking in/out of accommodations, time at train station, etc. as well.

I noticed you said you will "return your car in Prague." Unless you're venturing into the countryside, a car may not be needed as train is much more efficient and parking is a hassle in most cities.

Have you booked your flights? I highly suggest you consider flying open jaw - in one city, and out another (depending on your itinerary). For example, into Prague and out of Vienna. This will save you time and money getting back to Prague in the end.

I did a Prague, Vienna, Budapest trip several years ago, although all of our transportation was by train. Those three cities are a good grouping. If you're looking to spend a lot of time in the countryside, though, three large cities plus small country towns is probably too much for the amount of time you have.

In Vienna we bought a ticket package that took us by train from Vienna to Melk, allowed us entry into the Melk Abbey, boat cruise along the Danube river to Krems, and then train back to Vienna from there. It was a really enjoyable outing. I'm sure there's a way to do this by car. There were several little towns we saw from the boat that would be easy to stop in if you were driving this route.

I haven't been there, but I know Cesky Krumlov is a popular day trip from Prague.

With all due respect, your request for itinerary help is so very wide open, making it difficult to respond. "History, countryside, and food" is not much of a filter, either, as this part of Europe is brimming with all of the aforementioned.

I live in Vienna and could easily offer suggestions for a 16 day visit in my adopted country alone. Perhaps consult a few travel guides and narrow down that which truly interests you, and then return with more specific questions related to your itinerary.

Wanting to avoid a drop-off charge with a car rented in Country A and dropped in Country B does not dictate that you have to fly RT into one city. Given the destinations you have mentioned, nothing would preclude you from flying into Prague, using the car to explore a bit, then taking a train (or two) elsewhere, picking up another car, and returning it to that same country. If you did that, you'd avoid all the hassles that are going to come with "wanting to have a car the whole time."

But I agree, you haven't told us much, and what you have told us seems not entirely practical.

Lots of different options here, but taking a stab in the dark...

You could do something like this:

Prague: 5 nights with day trips to Moravian countryside/vineyards - a beautiful but often overlooked region in the Czech Republic - maybe a day trip to Kutna Hora or Telc, cute little countryside towns
Cesky Krumlov (one of the most stunning medieval towns in Europe, complete with castle): 1 night
Salzburg (adorable town with lots of countryside): 2 nights
Vienna: 3 nights with day trips to nearby countryside or vineyards (others can chime on in the best areas here)
Budapest: 3 nights
Drive or train back to Prague for flight
Prague: 1 night before flight

This itinerary might be a little hectic, so you could remove Cesky Krumlov or Salzburg and add more nights to the main cities (Prague, Vienna, Budapest) and just add on day trips. Lots of great countryside that's reachable from all those places, but I'm more of a city girl, so others will need to help with those suggestions :)

Can also do less days in Prague, add those days to Vienna or Budapest. I lived in Prague for awhile and am biased towards it, but others will say that Vienna and Budapest are bigger (which is true) and you might prefer more days there to explore. But this gives you a general idea of the KIND of itinerary/structure you could develop.

If you want to see more of Czech Republic than just Prague, then I agree with fleur de lis about Telc, Kutna Hora, and Cesky Krumlov. Also recommend Karlovy Vary for a very different experience. KV is known for its mineral springs and spas. It's a fun place to visit, and architecturally and visually, it is very different from Prague and CK.

Do you need Intenational Driving Permit to go along with your regular license? Some countres mandatory by law.