In 2002, we spent 3 nights in Berchtesgaden near the Hbf. The first morning, on the advice of our host, we went by bus to Wimbachbrücke, where we went up to the Wimbachklamm, a deep gorge carved by glacial water - cool and misty on a hot day. We came back to the bridge, had lunch, then returned to the Hbf, from which we took a bus to Königssee. We took the boat up to St. Bartholomä. Then we went up to the end of the lake and hiked over to the Obersee, and then took the boat back to Schönau and the bus to Berchtesgaden. We had dinner in Berchtesgaden. The second day we went by bus to Obersalzberg and took the special bus up to the Eagles Nest. We hiked around a little at the Eagles Nest, took pictures at the cross on the summit, had lunch at the Nest, then went back to Obersalzburg. We spent the rest of the day at the Dok Center, seeing the exhibits and touring the bunkers under Obersalzburg.
At St. Bartholomä on Königssee, the line waiting for the boat back to Schönau was long, but there was no line for the boat to the Obersee. At Obersee, there was no line for the boat back. When we got to St. Barts, there was still a long line for the boat back. We probably didn't spend much more time (and a lot less in line) by going up to Obersee rather than waiting for the boat back to Schönau.
The tour through the Dok Center in Obersalzberg was really worthwhile. It had a lot of historical information about the rise of the Nazis in Germany in the 30s.
In short, it would be worth spending a night and two days in Berchtesgaden. In fact, I saw everything I wanted to see in Salzburg in a day. Better, make Berchtesgaden your base and make a day trip to Salzburg.