Cheapest way to travel 3 countries (Germany, Switzerland, Italy)

These can all be done easily by train. Use www.bahn.com to get the schedules. Just input the dates and destination and you can see all the trains. Some can be purchased in advance, some no need to. The tickets should be bought from the individual country's rail websites. Since your lodging is fixed, you can commit to advance purchase nonrefundable tickets except maybe your arrival.

If you itinerary is locked in and you don't wish to venture out and see the countryside then just use the train. I drive 90% of the time and if it were my trip I would want a car to explore Germany , possibly Switzerland and most definitely the Tuscan countryside. Also it is beautiful to drive the area around Lake Como... now how you could negotiate all this with rental cars is up to you. A car would be a problem in CT, and Rome but other than that it all depends on how you want to see Europe. Just be aware if you do rent cars you will incur a big expense if you pick up in one country and drop in another.

Switzerland is fantastic but there is really no cheap option. Train tickets are pricey although the service, timeliness, and beauty of the trains reflects the price! If you rent a car, gas is crazy-expensive BUT in my opinion it's worth it to be able to get to the places you can't if you're using public transportation. So many beautiful villages you can't get to any other way and tiny, breathtaking mountain roads that will put you into some of the most gorgeous scenery you will ever see!

Thank you all for the responses. I think we may rent a car when we arrive in Frankfurt for about 3 days while we visit my cousin in Ramstein (doing day trip on Rhine River and visiting Trier), then train from Frankfurt to Fussen, Fussen to Interlaken Switzerland, Interlaken to Lake Como (I think we may have to take the train to Milan then Lake Como), Lake Como to Cinque Terre, rent a car in Pisa (which I think is the nearest town) and drive to Assisi (staying 3 days) then return the car to Pisa and take train to Rome. Since we've never been to Europe and we're going to lots of places, this might be best, cost wise. We don't plan to drive around, just walk or take local transportation around the towns we'll be staying in. We want to just absorb the people, culture and scenery - don't plan to do a lot of touristy stuff. Any more feedback would be appreciated, mostly about which rail pass to buy and when to buy (before we go or when we get there)? Information also on local trains, buses, etc. once we arrive off the train would be welcome (based on the cities I listed in my original query). These are the only cities we'll be visiting and staying in. We are complete novices and appreciate any help we can get. Thanks!

As long as you are renting a car, be aware that there is generally no penalty for dropping off a car at a different location as long as it is within the same country. So you could keep the car you rent in Frankfurt, drive to Fuessen, then drop it at a convenient spot in Germany near the Swiss border, and continue to Interlaken by train. In Italy, you will need to have an international drivers license, so start working on that now. I believe AAA can help you out there. So there would be no need to backtrack to Pisa to drop the car. You could drop at a convenient town with frequent direct rail service to Rome, say Orvieto, or even drive it all the way to Rome and drop it there (if you are brave). Also research any places you visit in Italy with the car for ZTL's. These are historic city centers where a special permit is required to drive a car. These zones are guarded by robocams that will snap a picture of your license plate and begin a long process of sending you a ticket.
You might want to consider getting some sort of Swiss pass, but it is maddeningly difficult to pinpoint the optimal one. There is a Swiss visitors 1 month Half Fare Card available for 120 chf per person. 50% off all trains in Switzerland. Forgot to ask is if you are traveling any children under 16. They may be able to travel free if you get a pass.

You have picked a very busy itinerary, especially since you've never been to Europe before.
After visiting your cousin, I would suggest you drop your rental car in Stuttgart and take a train south to Zurich and into Switzerland. (I'd suggest skipping Fuessen, as I assume you're just wanting to see Neuschwanstein.)
From Lake Como-Lugano, Switzerland area, you'd go thru Milan to get to the C/T. Most people catch the local train out of C/T to La Spezia where they change trains for points south--usually Pisa. I would suggest you take 1 hr. train ride over to Florence and pickup a car in a city center rental car location (not airport). It's an easy drive down the toll road/motorway to the Assisi area.
You could turn in the rental car in Orvieto and take a 70 minute train ride into Rome.
If you're especially budget minded, you could visit your cousin and then fly Stuttgart to Rome on GermanWings, a budget air carrier. Then you could reverse your itinerary after Rome taking a train to Orvieto where you could pick up a rental car. Then you could visit Tuscany, the C/T and fly out of Milan. I just hate to see you get so close to Florence and not experience the art, history, architecture and food that the city has to offer.

Walking would be the cheapest !!

Thanks Sam and David for the additional information! I think we might keep the car then to travel down to Fussen and then dropping off on the border and taking train to Interlaken. David - Unfortunately our itinerary/lodging is set and we'd like to stick to it. I do, however appreciate your info on going from C/T to Assisi. :)

I'd suggest a car in Italy, for the drive from Pisa area to Rome (turn in at main airport). Last year we got a rental car at Rome airport and it was fairly easy to get out of airport, around Rome and head up to Sienna, Florence, Verona, and other spots between, before turning the car in at Venice. We plan to do a similar trip this year but hitting different areas.

Additional charges for a different drop-off location may or may not be charged. I don't have much experience with it, but I've been looking at prices in Italy, and the cheaper companies (like Sixt) may not specifically list a drop-off charge, but the daily rates are significantly higher if I choose a different return city. And picking up or dropping off at an airport almost always costs more.

If you go to Priceline you can get a variety of quotes for the cars and hold those that look good without having to prepay (I never do). The rates change randomly... so if you have the time it is worth it to revisit the website, and make a new reservation if a cheaper one becomes available. I am going to Fl. next week and have changed my car res. 4 times in the last 2 weeks. The rate went from over 350 for 8 days to 162 for the same 8 days. I will watch again over the weekend and at that point may bid on the car in which case it would be prepaid, so no changes can occur. Usually though the price I get is reasonable enough that I would rather not prepay in case something happens. Just reserve now so you know you have a car and watch as the time goes on. How many are traveling?

There's only me and my husband travelling. I think what we've decided is to rent a car in Frankfurt and turn into a city on the German border, either Frieburg or Lindau. From there we will take a train to Interlaken, then to Lake Como and Cinque Terre. We want to then rent a car to travel to Assisi and then train to Rome. Two questions - (1) Which city in Germany, Frieburg or Lindau would be best to drop off car (we will be coming from Fussen) and which city is best to get a train to Interlaken? (2) We need a rental car on Sun. 3/18 but La Spezia does not have rental car places open on Sunday. Where can we go from Cinque Terre by train, to a city on the way to Assisi to rent a car on a Sunday (Pisa?, Florence?)? Any help would be appreciated.

Actually, Freiburg looks best as there are a lot of car rental locations right by the train station, and you can get an ICE train direct to Interlaken at 11 am, 1 pm, and 5 pm. Just under 3 hours to Interlaken Ost.
At Pisa, you can get a bus to Pisa airport from Pisa Centrale where they should have Sunday car rentals.

Thank you so much Sam! That is very helpful information. This is our first trip to Europe and I'm finding making arrangements for travel while we are there to be the most challenging. Appreciate you help!