My husband and I are planning a delayed honeymoon to Germany, probably 10-11 days, in April 2007.

We would definitely like to visit Munich and Berlin. But it might be more economical to fly into Frankfurt. We would also consider a side trip to Austria (or Prague), if it fits in.

Can anyone recommend an itinerary or how to travel (train, car, etc)? I speak a moderate amount of German to be able to get us around.

I appreciate any suggestions.

You should probably reply with a list of your interests - do you want big city, or small town/countryside, etc. Have you been to Germany before? If you spend most of your time in the cities, I think the train is preferable. Otherwise, driving is very easy and fun in Germany, and allows you more freedom.

That's really a very general question.

First, Frankfurt is a convenient base to reach both Berlin and Munich.

If you concentrate on towns and cities travelling by train is very fast and convenient. E.g. the train from Frankfurt Airport to Berlin takes 4h27m and to Munich 3h36. Both Salzburg and Prague are also convenient by train. See www.bahn.de for details. To visit the upper Bavarian castles (Linderhof, Neuschwanstein, Hohenschwangau) you may rent a car for one day or you book a bus trip from Munich.

Berlin is one of the world's most fascinating cities with world-class attractions and museums and with a bustling city life. Spend at least three days there.

I agree with Ky Bob - for big cities train's the best. And for your itinerary the bargain German Rail Twin Pass is a great deal - it starts at $150 p.p. for four days of unlimited travel in a one-month period with the option of adding on days at about only $20 a day - also comes in first class for about $200 p.p.
Regular fares Frankfurt-Berlin and Berlin-Munich would be much more than the pass price. And the pass can be used on any train at any time (with the exception of a handful on ICESprinter trains that few tourists would take). For schedules and prices in euros for point-point tickets visit www.bahn.de - the German rail web site. A good way to reach the English language schedule and pricing page of the German rail site is to go to: www.budgeteuropetravel.com and on their home page click on the link near the bottom of the page "All European Railway Schedules" (or some such wording) and up will pop the English page with two boxes where you just put in say Frankfurt and Berlin and a date and you'll get all the trains for that day and the pricing. The Budget Europe site also gives current pricing on German passes as well as suggested itineraries and links to the Rhine Boats and Romantik road buses which are either free (boat) or deeply discounted (bus) with the pass. I always also recommend them for passes for their expertise in German trains.
Your German pass will take you to Salzburg, Austria without extra charge, even though Salzburg is a few miles inside Austria - but there is a German train station in the Salzburg Hbf station so for pass purposes it's a German station. Pass also gets you to the Czech border and trains from there to Prague and back are very cheap.
The German train system is so great that you need not speak English a'tall to use it - info is posted everywhere and you just won't have any problem doing the train - many conductors and Germans speak some English.
As they say in German, have a Gut Fahrt (good journey!)

And as an albeit small perk for the railpass it's also valid on S-Bahn systems in cities like Frankfurt, Berlin and Munich. Now where you wouldn't want to use a day of your flexipass to take a few S-Bahn trips, if say you arrive in Berlin in early afternoon then you could use your pass for free S-Bahn travel throughout the city - like the classic great elevated S-Bahn line that runs thru the heart of Berlin and by many mega sights (Reichstag, Museum Island, along the Unter den Linden fashionable street, etc. as well as West Berlin's center around the Zoo S-Bahn station.
In Munich an S-Bahn line links the main train station to the Marienplatz, the heart of Munich's commercial district. And whilst these trips will only save a few bucks, not having to buy tickets, etc. and figure the system out your first day is an added perk. (You just need to board the trains as most S-Bahns have no turnstiles to go thru, you just walk on.)