Judy on our last 3 trips my family has traveled extensively in the areas you are looking at. Can I ask what you like in a travel destination, maybe age of people in your party, how active you prefer to be, generally budget level you are happy with? You name a number of great stops that to some extent favor different interests.
Also is it correct that you are only interested in trains? Many of the places you mention are quite close to one another and not a problem to link by car or train for that matter. If you want to go to Freiburg go! It's not far from Zurich Airport. My family loves Freiburg, but we love gnome-y Black Forest details (in the city even), bicycles, the mountains. It's as close to a sun-drenched relaxed college town as you'll get in German. But if you prefer a few more sights, a bit more urbane culture, better food and wine you want Strasbourg, 45 minutes away by car. Or the same but trading some of the urbane for storybook fantasy in lovely Colmar.
The previously mentioned Basel is a delightfully international city with charm and history. It's also flipping expensive (I joke to my wife it's the most diverse place we've ever been - Basel has every kind of very rich person in the world). I can't stomach USD $70 for two bowls of Vietnamese noodles and two beer at a "budget ethnic" restaurant, so for me it's a passing through place.
Garmisch-Partenkirchen, Mittenwald, Oberammergau: the first if you want more of a city with interesting small city things to do right up against the mountains; the last two for more of the mountains are the village vibe.
Anyway a profile of travel-style and interest would help!
Henry