I can only supply a little help. Berlin is a fantastic city to visit, the walking tour is really good but unfortunately too long for small children (over two hours). I stayed in this hotel about 7 years ago: www.hotel-johann-berlin.de/, at the time I was extremely happy with it. It is in the old eastern part of the city and within walking distance of the city centre. Check reviews on sites like booking.com & trip advisor and then make your decision.
I loved Salzburg but can't remember where I stayed but if I can find out I will let you know, as it was genuinely in the old Austrian style. At the time (some time ago) I remember seeing men playing chess with a giant chess set in the main square, which possibly the children would enjoy! You could also climb up Moncksberg there, the ruins of old monastery are at the top. Mozart's birth place in the city you could visit but it is just a small room upstairs in a house in the city centre. I do remember that the wurst (hot dogs with saeurkraut) from the street stalls in Salzburg were particularly good.
I have been to Munich but not since the eighties and in a camper van and don't remember much about it except noticing how good the cycle lanes were. Unfortunately I have not visited the other cities yet!

I do not know the specific geography concerning Prague, but I find that staying in a large city for the last night is not necessarily the most convenient way of traveling. This year we stayed outside Nice and dropped off the car at the Nice airport on our way home. A small town outside Prague might be an easier stop than driving into the city, parking, getting the luggage to the hotel, etc. This is assuming that you can drop off the car (you are traveling by car?) at the airport.

Munich is a bigger city than Salzburg and needs more time than you give it.

If possible, perhaps a much better use of your time, is to fly into Berlin and out of Munich. It's a very busy itenerary with children and your mother, but consider.

So, Berlin [2.

Dresden [2]

Prague [3]

Chesky Krumlov [2]

Salzburg [3]

And Munich [1]

On this site you will find some of the cities with good information. www.inyourpocket.com

Agree with Michael; That last night that you had one night in Prague, you could add to Munich. So, Munich [2].

I feel you have too many places in 2 weeks. You will be spending a lot of time in transit from place to place and packing/unpacking. It takes time to acclimate yourself to a new city.

I would not break up your stay in Prague. Visit Prague at the end of the trip so you're in the city you're flying home from. Arrive in Prague and immediately leave for your first destination.

2 nights in Berlin is only 1 day. It's too far to travel and offers so much to see that 1 day will cover very little.

You'll only have the afternoon in Munich and then have to leave for Berlin.

You need to consider your children and how they will feel being dragged from one place to another and always waking up in a new hotel.

You've referenced someone else's trip but did you notice that they stayed in each place much longer than you're planning to do and did not go to as many places. And, they did not have young children with them.

A couple of notes:

You are wasting time by flying in and out of Prague - fly open jaws into your first city and fly home from the last - it won't cost any more. You need more time in Berlin and Munich (which have much more to see than Salzburg - although the latter is a charming town.

If it were my trip I would do it by car - which I think is easier with 2 small kids - less tied to schedules of public transit and can stop and let them run around somewhere when they get antsy. It may cost more - and there will probably be a drop-off charge, but IMHO the extra cost is worth it.

You don;t say when you are going - and I hope it isn;t soon - or you will have lots of trouble with accommodations. With 5 people an apartment may meet your needs better than 2 hotel rooms - but typically you need to reserve far in advance and many require a specific number of nights.

Overall, with 2 little kids I would try to simplify the trip - and make sure some of the places you stay are near parks/ playgrounds.

Actually, you could travel by car and perhaps for less money. If you consider the itenerary I suggested, hire a car when leaving Berlin. Drop the car off in Munich, no drop off fee.

I have driven in all the cities except Dresden and it is doable as the 'nytraveler' suggested.

You need to look at a map and then plan what is best for you and the family. You can check the distance between cities on this site. viamichelin.com

Are there any issues taking a German car into Czech Republic? I know that Austria is fine, but there are restrictions for certain countries.

I do agree with flying open-jaw, adding more time to Munich (with only 1 night, you might as well leave it off completely), and trying to trim something from the itinerary.

Good point; I have driven those countries in the early 2000's, but I alway check with the actual car company. Ask the question by e-mail and require an answer so that I have back-up information. Never by calling.

Most recent was in 2009, but only renting at the Munich airport, driving into Austria and then back into Germany, eventually returning the car to the Munich airport.

Much appreciate.

I have some limitations on my Fly in/Out city. No changes can be made on Prague Arrival/Departure.

I dont mind dropping few of the German destinations especially Berlin and Dresden. (I could Keep that for the next trip).

There is less chance that I would visit Prague any time soon.I would prefer to visit must see places in Prague(dont mind if its towards the end) and I hear Cesky Krumlov is good place too.

Since I would be visiting C.K., I thought I could cover Salzburg/Hallstatt and then cross to Germany- Would visit places close to Munich. Finally I could go back to Prague from Munich either by Train/Flight

It would be very helpfull if any bettersuggestions for apartments/places to visit or order of visit etc. I dont mind revising our itenrary.

Many Thanks

You have helped solve an itenerary. You could still drive.

Prague [2] Chesky Krumlov [2] Salzburg [3] Passau [2] Regensburg [3] and back to Prague [2] Still a lot of stops. I don't think any of these would be more than a three hour drive.

Pick up a car when leaving Prague and drop it of when returning to Prague. Consider Skipping Berlin, Dresden and Munich.

Still need to look at a map of Europe.

Definitely keep Cesky Krumlov in your itinerary. I would do Prague 3 nights and not less (especially to accommodate jetlag from arrival). I did 4 nights in Salzburg, which was way too much, and I ended up having too much time on my hands. Plus, the ice caves nearby had just closed for the season when I arrived, so I could not do that to kill time. But with kids, I'm sure you're considering a half day trip to the salt mines, which would be easier than the ice caves (heard there is a lot of walking with the ice caves) If pressed for time, maybe just do two nights in Salzburg. Everyone is different but I enjoyed Salzburg the least out of my visit last year to Prague, CK, Salzburg, Vienna, Budapest.

You can also strongly consider dropping Berlin and keeping that for another trip. Dresden can be combined on this trip with Prague or on a future trip with Berlin. If I had to drop one city out of your current itinerary, I would drop Berlin.

Thank you iris1745. Do you have any suggestions on places to stay in your reccommendations. I would prefere an apartment /B&B.

nomadder, Most of the people were suggesting 1 day in CK. Do you have any suggestions/links for places to stay in CK & SalZburg.

I want to visit/stay in Hallstatt for a day.but no idea where to stay or worth the hassle or should I do a day trip from Salzbug.

Quite confused with German side of places to visit and getting back to Prague for our departure.

Anybody knows how good is this place is NATIONAL THEATRE APARTMENTS Ostrovni 7, Prague 1 - Nove Mesto, The Czech Republic. 120 Euro per room/night

http://www.prague-city-apartments.cz/product/about_en_NATIONAL_THEATRE__APARTMENTS.html

In Cesky Krumlov, I stayed on the outskirts of the town at Pension Amadeus, which is an easy 5 minute walk to the town square. I would stay there again. I was there as a solo traveler, so I am not familiar with their larger room options.

http://www.penzionamadeus.cz/indexa.htm

I stayed in CK for two nights, which is a very leisurely stay. One night is doable but would be too much of a rush in my opinion when taking in travel time. CK is a place where it is nice to be leisurely, stroll the cobblestone streets, explore the castle and the beautiful views. There is a marionette museum if you are into that, but it is just a bunch of hanging marionettes and not much else as far as detailed explanations of marionette making, etc. Maybe stay two nights and leave early the next day to Salzburg. I took one of the coach services to Salzburg and it was about a 3 hour drive if I remember correctly, but we stopped in Linz to drop a couple off.

In Salzburg, I stayed at: http://www.weissetaube.at/en

It was a decent price compared to other places and a nice, cordial family-run hotel. I would consider staying there again if it was the best-priced hotel I could find. Easy walking distance to major sites. Nothing fancy but nice staff. By the way, Salzburg is clean and beautiful but more monotone and for me was anticlimactic after being in the colorful, old town, gothic CK. But it is a completely different type of town and experience. From my research I think Hallstat can be a day trip from Salzburg. I did not end up going there so cannot speak from experience.

nomadder many thanks.Looking forward to visit CK.

yes planning for day trip to HallStatt.

Bad luck your suggested places were full too.