Freiburg to Munich on the train, advice on 2 day stopover?

Leslie, My top two suggestions would be Heidelberg and Baden-Baden. While Heidelberg doesn't look "between" Freiburg and Munich on the map, many of the ICE (high speed) train connections go through Mannheim, which is only about 15 minutes from Heidelberg. Rick Steves has a prejudice against Heidelberg and doesn't include it in his guidebooks, but many others (including me) consider it one of their favorite places in Germany. Rick on the other hand does like Baden-Baden a lot, and I believe you can read about it on this site under "Plan Your Trip." It's a calm, attractive resort town famous for its spas and palatial casino. Good luck / Gute Reise!

Lindau isn't exactly halfway, but it makes a good intermediate stop. You can take the Rhein up to Basel and follow it to Bodensee, via Schaffhausen and Rheinfall and along the Bodensee to Lindau. That will take about 4½ hours and you can do it with a Baden-Württemburg ticket for €29 for both of you. Spend the rest of the day, and the next morning enjoying Lindau, then go the rest of the way to Munich (3 hrs or less), again with regional trains and another €29 Länder Ticket (this time a Bayern-Ticket). Alternatively, and a route I might prefer, would be from Freiburg through the Black Forest, via Titisee, to Donaueschingen, the headwaters of the Danube. From Donaueschingen, follow the young Danube via Beuren to Sigmaringen, where there is a very old Hohlenzollern Castle. Spend the night in Sigmaringen. I would suggest Hotel-Gasthof Traube, which was built in 1722. Then go from Sigmaringen to Ulm (climb the world's highest Gothic church tower there), and on to Munich.