The champagne region is very beautiful and a nice day trip from Paris. Wansee, a Berlin suburb where the final solution was formulated, is an interesting side trip just 45 minutes away on the U-Bahn.
Walking tour in Berlin. Will see all of the modern history you have read about.
Dacau concentration camp near Munich. Neuschwantstein and Hoenshwangau castles, Glockinspiel tower clock, Chimsee, Salt Mines near Salzburg, Garmisch-Partenkirchen, Eagles Nest,
Paris - go to Wiki. Too much to list. Starbourg is on your way to Munich. Nice cathedral there. You might also want to stop in Stuttgart for the day to eat and walk old town.
Paris is the best city in the world, IMO. I spent three days just wandering through the various neighborhoods, hopping on and off the metro, and just exploring, with little if any specific destinations in mind.
That is my recommendation. If you can't find something to interest you there, then you aren't alive.
Thanks for the replies everyone. I'm not worried about the cities, just wondering if I was missing anything not checking out what was in between the cities.
Strasbourg is a very cool town - it has changed hands so many times, it's not really French or German. Everything is in both languages and it has an awesome downtown/square area (can't remember the name of it though).
The Topography of Terror in Berlin was an unexpected thing that we came to get a lot out of. It is on the sight of the Gaspato prison were people went before they were sent to the concentration camps. Very moving. It is also along the longest standing piece of the Berlin Wall.