11 day trip this June Waakirchen, Salzburg, Wengen

I wouldn't do both Schilthorn and Jungfrau excursions. The latter uses up pretty much a whole day and is very expensive so I prefer the Schilthorn.
Wengen is great, but Murren has more hikes starting there--zero compared to four. To see all my recommended hikes in the whole area, click on my name and I've described them in previous posts.

I see one small catch in your plan. You are picking up a hire car in Munich and returning it at Zürich airport. Picking up a rented car in one country and returning it in a different country usually incurs a large surcharge or is not allowed. I suggest you get a quote for this car, including all surcharges, before you finalise this plan.

Also, you cannot drive to Wengen, it has no roads. You would have to leave the car in Lauterbrunnen in the valley bottom (paid parking) and take a train up the valley side to Wengen.

Salzburg - Füssen (Neuschwanstein castle) - Wengen. follows the north edge of the Alps. Small slow winding hilly roads, but scenic. No Autobahns until you get into Switzerland.
According to https://www.viamichelin.com/ Salzburg to Füssen is 03h26 for 221 km, Füssen to Lauterbrunnen is 04h43 for 368 km. Both times with no allowance for stops. It would be a long day.
This route is equally difficult by train. The route via Innsbruck is Autobahn, and faster by both road and rail. Viamichelin says 06h54 for 563 km,

Finally to drive on Autobahns in Switzerland or Austria you need to buy an "Autobahn Vignette" which is a sticker to pay the tolls. The Swiss Vignette costs CHF 40, I don't know the price of the Austrian one. Autobahns in Germany are toll free.

P.S. make sure your hotel in Salzburg has parking, or find out where nearby you can park. Most hotels in city centres will not have parking.

Thanks so much for your detailed responses. I am trying to do the math and by my calculations it is still probably cheaper to rent a car for a family of four even with the drop off fee. Hertz gave me a quote of $500 total including drop off fee unless I am missing something? Because we have to pay for 4 train fares from Salzburg to Lauterbrunnen and then train fares to Zurich from Lauterbrunnen it seems to be cheaper to rent a car. Obviously I am torn on this decision between car rental or not. We love to stop along the way which a train will not allow us to do but I worry about the stress of driving. How bad will traffic be beginning of June? We should get plenty of time on trains, gondolas, etc. while staying in Wengen I presume? But I hate to miss out on the Swiss public transport experience. I hope someone is up to the math challenge of fares. :)

Shananraines, are any of your family of four under age 16? If so, you can buy a Junior Travelcard for 30 Swiss Francs (or 15 francs on sale until January 31, 2018) for each of them, and they can travel with you on public transit for free.
https://www.sbb.ch/en/travelcards-and-tickets/railpasses/junior-travelcard-children-co-travelcard.html

Thanks, but they are both over 16 so we have to buy four fares.

Overnight stop - Lindau. It is (nearly) on your route from Füssen to central Switzerland. It is a lake-side town on Bodensee (aka Lake Constance) The old part of the town is on an island in the lake reached by a bridge.
Town website: http://www.lindau.de/en/

If you want to avoid the international car drop-off fee, Lindau is the last town in Germany. You could drop off the car there and proceed into Switzerland by train. Not sure if that would be cheaper or not for your 4 people.

The Austrian Vignette is for 10 days and last time I got one last autumn it was €7.90. The Swiss one is CHF40.

Unlike in Switzerland where the Vignette covers all highways, in Austria there are a handful of private highways with tolls not covered by the Vignette, in the mountains mostly, and there are several tunnels on the autobahn between Salzburg and Switzerland which are quite expensive and not covered by the Vignette. One bridge too, the one between Innsbruck and Italy.

Unless you stay out of town at a hotel in Salzburg who has parking, tourist parking is expensive in Salzburg. Going rate at the remote car parks is €15 per day (fixed cost) plus local transportation. It is also that price to park under the mountain but there used to be a deal that if you were there for less than 2 hours you could get the parking ticket stamped at a few Altstadt businesses and get out for €5. Can't go over the 2 hours, and it can be a bit of a walk from the carpark through the mountain to your destination.

Train from Bavaria (anywhere in Bavaria) to Salzburg is around €30 for the whole family, for the whole day.

You will be lucky to be so close to Bad Tölz, one of my favourite places in the whole area there.

I know you have checked, but the amount you are quoting sounds very very low to me for an international drop charge. The company can't rent it in a different country than it is registered in and they have to hire somebody to return it to the original country. The loss of opportunity plus the repatriation costs are what add up to the drop charge (plus a bit of profit).

I will do more research on car rentals but the highest drop fee I saw was $250. Weirdly, plane fares are $50 cheaper per ticket to fly into Munich and out of Zurich (rather than round trip to Munich) so we would be making up the difference with that itinerary. I am going to keep crunching numbers.
Can someone comment about traffic in beginning of June around those areas?

Thanks for the suggestions on other places to visit. Why is Bad Tolz your favorite place? I see if is 15 minutes from my friends town so we will definitely go visit!
Thanks again for folks taking the time to help me figure this out.
Shanan

I like Bad Tölz for the river views, the bridge, the park the other side of the bridge, the gentle hill uphill on the main road, the bakery at the top, the view down the hill, comparing the gelato places on the way up, the back roads at the top, and the general ambiance.

Nothing special just a really nice place.

There is always traffic around Munich. Do you use a smartphone? iPhone has a Staufinder app which is very good but I don't know if it is on Android or Windoze Phone.