This June I will be taking the train from Zürich to Munich to Salzburg. There are stops in Germany at Lindau-Reutin, Memmingen, Buchloe, Rosenheim, Prien am Chiemsee, Traunstein, and Freilassing. My 13th ed. Germany guidebook doesn't mention anything about these towns (except for showing Herrenchiemsee castle on the map), but I am hoping that the forum's experience can help me find which of these towns to visit.
Lindau is very pretty (on the shores of lake Konstanz), but Reutin station is not very central - you would need local transportation to the island where the town center is located or walk 20-30 min.
Otherwise I do not know. I hear Chiemsee is a beautiful lake but i have never been!
It's not clear if you are travelling from Zurich all the way to Salzburg on the same day. If you are, maybe Memmingen, as long as you can catch another train soon enough.
If you have a night or two to break up the journey then a very worthwhile stop is Lindau, a smallish waterfront town of attractive buildings and streets (a quick stop doesn't give Lindau enough justice). Memmingen has a decent, compact centre but not worth an overnight stay for me.
From Munich to Salzburg, Chiemsee is worth stopping off at for the palace and the smaller abbey island (Fraueninsel): this can turn into a whole day affair.
North of Memmingen , (roughly) is what I would suggest, the town of Ulm, well known for its cathedral (das Ulmer Münster) in Germany.
Another vote for Lindau, but for an overnight or two.
Lindau and Chiemsee. Both seriously nice places to spend time.