Itinerary help! Rothenburg, Bavaria, Munich, Salzburg route?

"How should we plan our time to hopefully see Bavaria, Munich and Salzburg?...Recommended home base in Bavaria?"

First of all, let's clarify the geography. Bavaria is a huge state that stretches almost to Frankfurt in the northwest and includes Munich and Rothenburg. If one wished to see all of Bavaria, a single base won't work - it's just too large.

"We can rent a car if necessary." Don't worry - it's not, as you can see from this rail line map. If by chance you pick a destination without a station, it's likely tied to the rail system with a bus connection.

Recommended home bases: It's possible to cover much of northern Bavaria from a base in Nuremberg (a major train hub and quite a nice city.) In the south, Munich (or maybe Augsburg) works pretty well. But neither of these will cover all destinations. Not that that should be a concern - you don't have time to see EVERYTHING anyway. But if your point is that you'd like to minimize the number of places you stay, I'd begin looking at destinations within traveling distance of Nuremberg and Munich and consider 3-4 days in each. Some suggestions:

NUREMBERG BASE day trip possibilities (none of these destinations is more than 1.25 hours away.)
Bamberg - Würzburg - Iphofen - Bayreuth - Rothenburg - Bad Windsheim (great open-land museum) - Regensburg

MUNICH BASE day trip possibilities (up to two hours away)
Augsburg - Landsberg - Landshut - Prien and Herrenchiemsee - Füssen - Mittenwald - Garmisch-Partenkirchen - Salzburg - Dießen - Herrsching and Andechs Monastery - Regensburg - Nördlingen - Burghausen

Getting to any of these places is easy when you buy a regional day pass. There are dozens of different regional day passes good for regional train travel within Bavaria, but one day pass that covers all of Bavaria - the Bayern (Bavaria) Ticket - which includes Salzburg and costs €28/day/couple. The other day passes are valid within various subregions of Bavaria and cost less. For example, the day pass for the Nuremberg region (called the Tagesticket Plus) costs €18.70/day/couple and gets you to all those destinations listed above but Regensburg (use the Bayern ticket instead.) Some day passes like the Bayern Ticket have hours restrictions (like after 9 am if it's a weekday) but others do not (the Tagesticket Plus, for example - which has an additional perk - it's valid for both Saturday AND Sunday if you buy it on Saturday.)

So I'd start by looking to see what interests you in some of the destinations named above.

(Don't mean to diss your plans but do understand that Rothenburg is one of Germany's most touristy and tourist-packed enclaves; its streets are routinely overloaded by the 2.5 million tourists it gets annually (tourism is the only game in town,) everything's in English, and as Rick says, "Rothenburg is well on its way to becoming a medieval theme park." If my best friend had 7 days to see the real Bavaria, I'd send him elsewhere.)

I like the advice above. I would also mention that I think Salzburg is worth being a base for a few days. There is enough to see there for at least one full day. I really enjoyed being in old town at night with all the fountains and th fortress lit. Very pretty. It's also a good base for some day trips into the Austrian alps or Berchtesgaden in Bavaria. Rothenburg is very touristy, but I still enjoyed it and didn't find the crowds too terrible, especially late or early in the day. Take the night watchman's tour if he is still doing them. Very entertaining.

The area around Nürnberg is one of my favorites in Germany, so I like the advice that Russ gave. However, when a lot of folks say Bavaria, they mean southern Bavaria = Alps. If that is the case, you might take a route more like:

Rothenburg, Regensburg, Salzburg, Garmisch (or?), Munich and fly out.

Thank you for your help. I should have clarified and said the alps castle region (Fussen, GP, etc) when I said Bavaria. My mistake.

I am one of those people who would suggest getting a car if you want a little freedom and spontaneity in your trip. It is a beautiful area to drive . The scenery is gorgeous and you can just take a few little side roads and discover some charming towns. I have driven here often and some of my favorite memories are those out of the way roadside picnics, or stopping to take pictures of a poppy field we spotted from the road. I am a photographer so I really like to be on my own schedule... To watch the sunrise or sunset from a particular vantage point... But even if I did not want to photograph I do not like being tied to a schedule. You will not need your car in Salzburg, but there are plenty of hotels with parking and the drive there from Munich was lovely.
I also suggest Bodensee (lake of Constance). It is one of the most beautiful places I have been.

I am in the midst of planning a trip to same locations and just wanted to mention that there are no car rental facilities in Rothenburg so if you took Gary Mc's advice which sounds nice to me- you would need to get car in Nuremberg or Regensburg (I know Nuremberg has plenty of car rental choices not sure about Regensburg).

You can drop car in Garmisch or Freillasing- (no need for car in Munich) maybe do this:

Nuremberg 1 night get car
Drive to Berchtesgaden area and base there for 3-4 nights- with day trip to Salzburg (no need for car in Salzburg)
Drop car in Freillasing take train to Munich for 3 nights