We are planning to do the Switzerland tour in the fall, and looking at maybe 4 extra days post tour to see some of France near the Swiss border. The tour ends in Bern. I have read that Annecy is beautiful, so that may be an option. According to Rome to Rio, it’s a 3 plus hour train ride. We have not rented cars so far on out trips to Europe, and I will be 70 by the time we depart. Seems I have read that age may be an issue with car rental, so we are initially looking at locations served by train. Lyon may make the most sense for departure airport. I have gotten good feedback on this forum before, so I thought I would throw a question out. The tour dates are set, so no flexibility there. Only question is where best to spend a few extra days at the beginning of October.
I think Colmar make the most sense. Fall is the grape harvest time. Colmar would be 2 hours with a single train connection in Basel.
It would be helpful to know what activities and things interest you (cities, villages, mountains, lakes, museums, wine, hiking, etc) and where you will have already been on your tour.
Have you already booked your flights? If so, where are you flying home from? As the previous poster asked, what are your interests.
Sam's idea of Colmar is good. You can easily spend a few days without a car. To visit a couple of wine villages in Alsace you could use the Kutzig Bus or book one of the excellent day tours with L' Alsaciette or hire e-bikes. Spend your last night in Paris before flying home. There is direct TGV service to Paris in just over 2 hours.
As I noted in my initial post, we are doing the Rick Steve Switzerland tour…itinerary is available on this site but includes Luzerne, Lugano, Lausanne and Murren as well as Bern. After all that, I think this would want a relaxing time enjoying wine, good cook and walkable towns prior to heading back to the States. Our return airport depends on which direction we head from Bern. We have been to Paris, so if we head south to Annecy Lyon looks like an option and another place we have not visited as of yet. I hadn’t considered it, but Colmar can be another option for sure.