Salzburg is beautiful. You might do the Sound of Music tour. The tour drives through some amazing scenery - lakes/mountains/adorable houses, etc. The toddler would like it because there is singing on the bus and places to get out and walk around, without TOO much walking. :) If you are a fan of the movie you shouldn't miss it. Just walking around the town of Salzburg (and getting an amazing dessert in one of the cafes) is charming, too.
There is the lovely Nymphenburg palace in Munich with gardens that you would all probably like.
Neuschwanstein is cool and so is the right-next-door Hohenschwangau castle. Get reservations ahead of time. You'd have time to do these castles in the morning and get back to Munich in time for dinner (at the beer halll!)
Berchtesgaden National Park (containing Lake Konigssee) is a beautiful, gorgeous park right on the way from Salzburg to Fussen. If you like mountain scenery, that's the place.