advise for eastern France/Western Germany

You need to know approximate travel times. There is a place on this website that tells you how to do that.

Briefly, for train travel times, go to the bahn German website and look up schedules. Remember that train travel time isn't just the rail time, it includes getting to the station, waiting for the train, same thing on destination side, and same thing going back to your home base, if you're doing a day trip.

For car travel times, go to viamichelin or rome2rio websites. Those travel times are road time only and don't include any stops.

A helpful general rule of thumb is: to get 1 full day of sight-seeing somewhere, you need to spend 2 nights, 3 nights = 2 full days.

Travel times are critical to your itinerary, many inexperienced European travelers under-estimate travel times, which means really late nights or missed train connections.

Sorry, it's not like here, where you just rent a car and it's easy and economical.

I had previously looked on the DB website for trains and there does not seem to be any direct train trips -it takes hours and switching trains, except the one from from Colmar to Strasbourg. For instance Strasbourg to Freiburg goes to Basel first. Is the problem because it is going between two countries? I was hoping there was some other travel option that was more direct.
Even the driving website - michelin seems to direct driving around the Black Forest rather than through it. Mapquest seems to offer different, shorter route alternatives for driving, but is it as accurate as Michelin?
Does it make more sense to stay in France for Colmar and Strasbourg and then move to someplace in Germany for the rest?
In renting a car, Dollar and Eurocar are much less expensive than Avis and Hertz. It seems to have something to do with insurance coverage, reading the website it is not clear. This didn't seem to be an issue when we rented cars in England. Is there something I am missing?

To answer some of your most recent questions:

If you establish a home base and then try to do day trips that are too far away from it, in terms of travel time, it's self-defeating because you spend most of your time looking at the inside of a rental car or train, instead of seeing and doing what you went all that way to do. This is why your reasonable estimation of travel times becomes so important.

Often travelers find that using 2 home bases instead of 1 results in a better quality experience. But it depends on the distances you're trying to cover in a day.

Many travelers feel that for driving in Europe they want to be fully insured, and that their US insurance doesn't adequately cover them in Europe. It's a judgment call based on your circumstances.

We have a few regular contributors who are, or were until recently, residents of Germany and Switzerland. Hopefully they'll reply to your questions about travel in Germany--right now it's getting a little late in Germany.
We don't have anyone who is a resident of eastern France.

I think a car makes sense in that area as some places are easier by car, For example the "Route des Vins" in Alsace.
For big cities (Strasbourg, and Freiburg-im-Breisgau), a car is a problem. For Freiburg-im-Breisgau (a lovely city), I would use a park-and-ride.

By train, you don't need to go from Strasbourg to Freiburg via Basel. You can go via Offenburg, takes just over 1 hour and costs €28. Do not be afraid of "switching trains", it is not a big problem.
Michelin tells you to drive around the Black Forest because that is quicker. Driving through the Black Forest is slow but prettier.

I would recommend Colmar with a hire car. Check your hotel has parking. and use park-and-rides for Strasbourg, and Freiburg-im-Breisgau.

Chris, thanks for the help on this.
I'm sure the original poster appreciates your local knowledge.

I have been too all those places more than once. I usually fly into Amsterdam as well. I ALWAYS rent a car. And I generally spend my nights as I go. The places you want to see are going to take you longer than you think when you count in stopping to sightsee, eat, maybe get lost or suddenly discover something you didn't know was there. The time it takes to get to somewhere, see it, and then get back to your "home base" is too much. I have never had any problem driving in any European city except Prague. I would not hesitate to drive again in the ones you list. But take a GPS and get full insurance. And don't drive if you've been sampling wine or beer. Also, with three of you traveling, a car will be less expensive than a train.

Thanks for all of the replys and suggestions.
After looking at the Euro-rail tickets for Germany and France, we have altered our plans somewhat. The train from Amsterdam to Colmar goes through Paris so we decided that we could not be in Paris and not stop. We still plan to stay in Colmar but less time, visiting Colmar, Strasbourg and perhaps Freiburg and then move on to Munich.

Questions about the Euro-rail multi-day ticket:
The train from Amsterdam to Paris stops in Rotterdam and then you can remain on the same train until Paris - the same is true of the train from Geneva to Paris. Can the conductor activate the pass when you enter France or do you have to leave the train and reboard? If you have to leave the train, how much time to allow to get Euro-rail pass activated? Any suggestions on how to handle this for both Geneva to Paris and Amsterdam to Paris?
We figured given the train prices bought individually, it looked like the pass would make more sense particularly if we could include the initial train ride to Paris also.

Thanks, in advance for any advise.

I think you had best forget Raileurope, as least as far as getting real rail options. They want you to go through Paris, because it is one change and Raileurope is owned by the French railway company, but there are many other options they don't show you. If you opt for a Eurorail pass, you will still need to pay a big reservation fee on the Thalys train to Paris, and a reservation fee on the TGV to Strasbourg plus walk a half mile from Nord to Est railway stations in Paris (or take a taxi).
You can travel via Utrecht, Frankfurt and Offenburg in about the same time.
Get schedules from www.bahn.com to see all your options.

Amsterdam to Colmar you do not have to go via Paris. Thre are two other options:
1) Change at Brussels, there is a train that goes Brussels - Luxembourg - Strasbourg - Colmar - Basel - Zürich
2) Take the Rhine route: Amsterdam - Cologne - Frankfurt - Karlsruhe (change) - Strasbourg (change).

Where are you looking up your train times? I hope it is www.bahn.de

Are you sure a pass is a good idea? If (as I think) you are only making a few rail trips, individual tickets booked in advance are usually cheaper.

Geneva to Paris is not an international journey, it is 100% SNCF (French Railways). Geneva station is a joint SNCF / SBB (Swiss Federal Railways) station.
Amsterdam to Paris trains stop in Rotterdam, Antwerp and Brussels. But there is no way you can get off the train and get on again. They only stop for long enough to let the people off and on, less than 5 minutes.