Day Trippin'

1. Dresden is worth a stop. It's an easy tram ride from the train station to see the city, too far to walk. I'm pretty sure you'll have to buy separate tickets from Berlin and to Prague. Try to squeeze as many hours as you can - lovely place.

2. Berchtesgaden: The Documentation Center is very interesting, especially the movie with interviews of town residents, then visit the bunkers - incredible. The day I went, the place was enshrouded in fog, so I didn't go up to "Eagle's Nest" but from what I read, there's not really anything of historical value there. Going up costs a lot, takes a good deal of time, the road is an engineering feat, and then there's the view. I got a bus back to the train station and took another bus out to the Frielicht museum and spent the afternoon there - highly recommend it. Then I had an overnight visit in Hallstatt. The beautiful views are early and late in the day (and only if it's clear - which it wasn't). I think Hallstatt is much more touristy, I wouldn't recommend it as a day trip.

Cesky Krumlov is a fairly long day trip from Prague though not impossible But as someone who has visited the Pilsner Urquell brewery 5 times then I would say go there.
The train stops only a few minutes walk away , you will see the brewery on the right hand side of the train as you approach the station.The tour is pretty good and quite long(It is a big place) the restaurant in the brewery itself is huge and very good , there is also a great shop there.If you want to continu the beer theme then there is a great brewing museum about a 15 minute walk from the brewery and it is easy to get back to the train station from there. there are also many other things to do in Plzen.
When are you visiting I am back there with a small walking group 5th -12 August and may take another trip to Plzen depending on the wishes of the group.
As to Berchtesgaden I was last there a few years ago as a day trip from Kitzbhule and a lovely place it is ,we also did the eagles nest tour from there.
Now whilst we are on the beer theme how long do you have in Prague, there are numerous micro-breweries in the city and surrounds and I can help you get to a few of them.
http://www.praguebeergarden.com/
http://www.praguebeergarden.com/pubs/category/microbreweries
this website is great for all things beer related and there is a list of micro-breweries on it so have a look.any you fancy let me Know and I can give directions on how to get to them.

You can stop in Dresden on the way to Prague on the same ticket. On the DB site, just check the intermediate stop box, Type in Dresden for the city and the # of hours you want to stop. You will be routed with a connection on to Prague from Dresden after your selected # of hrs has passed.

if you are into WWII then look up the Hydrich assassination, some interesting stuff to visit in Prague regarding that.Also just outside Prague is the Lidice memorial the village that was completely destroyed in the aftermath of the assassination.
http://www.lidice-memorial.cz/en/
easy to get a bus out there from Prague takes about 20 minutes from Nadrazi Veleslavin

Are you going from Prague to Salzburg? Have you thought about stopping in CK along the way? Maybe look into one of the shuttle services - Bean or CK shuttle. It might be more efficient.

Thanks for all the replies everyone! I think we'll do Dr's den as the intermediary, plzen over ck, I'm still on the fence about hallstatt/berchtesgaden. We are going from prague to vienna before salzburg or I would have loved to stop over on the way. Unclegus, we'll be there from mid sept-early october, thanks for the beer advice, that's one of our priorities on this trip!

A tip I got here a few years ago that was very helpful, so I'll pass it along: for the Berlin to Dresden and the Dresden to Prague trains, get seat reservations. These trains get very crowded, and having a reservation means you will have a place not only for you, but also your luggage (just above the seat). If you're standing in the aisle, you may not have a place to put the luggage. It was well worth the few extra euros.

Dag any help you need regarding beer and places to drink it in Prague just ask,There is a separate RS Czech Republic forum for specific questions that others may be able to contribute too and you can find me on Trip Advisor Prague forum most days.