Berchtesgaden or Salzburg

Depends on your interests.

There's more to see in Salzburg so that would be a better home base. You can easily get from there to Berchtesgaden for a day trip.

The weather may decide for you. If it's overcast and raining, a day would be wasted in Berchtesgaden.

I'm probably in the minority here, but I found Salzburg underwhelming. Given the choice (on a day with good weather), I would prefer Berchtesgaden.

Well actually a rainy day is perfect to visit the Berchtesgaden Salt Mine. You know you can do that trip (Munich -> Salzburg) super cheap and easy with a Bayern ticket, right?

How many nights do you have for Berchtesgaden/Salzburg? It seems you are driving from Munich to Salzburg and staying just 1 night and are asking if you should visit Berchtesgaden on the way. If all that is so, thought call. While we love Salzburg, we always stay in the Berchtesgaden area for our visits, as Salzburg is just a 30 minute drive away. This way we can stay in gorgeous alpine scenery.

they couldn't be more different. One is a high baroque city. The other is Yosemite in lederhosen. Both have historic sites, but unless you particularly desire the Nazi historical sites in B'gaden the choice is are you a country mouse or city mouse?

I would stay in Salzburg but go to Berschesgaden and do the Eagles Nest tour recommended in Rick's book even if it is overcast. I don't think it runs in the winter. We did it last September and if you love history it is four hours of complete fascination. The salt mine tour was just kind of ok. Since you have a car. It is an easy drive from Salzburg but the public bus works great.