Help with Planning Germany Trip

A couple of suggestions:
1. The Rhine/Mosel. We stayed in Bacharach for several days, exploring castles and hiking through the vineyards. Bacharach is filled with tourists during the day and very quiet at night, but we found a couple of nice restaurants (we didn't mind the quiet, since we hiked a lot during the day and were quite tired). There are some trails that connect a few of the castles. The train goes right through town, so it's easy to navigate the area.
2. Dresden. A lovely small city, with some very nice museums and almost no American tourists. We stayed in Dresden on our way to Prague, which is definitely worth a visit.

I'll second the vote for Dresden. If you're doing Berlin and Prague, it's right on the train line in between the 2.

If you're doing Berlin as a home base for a few days, take a day trip out to Pottsdam. Very cute city, lots to see there.

How far is Prague from Berlin? I think I would like to spend at least 3-4 nights in Berlin.
Could we see Dresden in a day then on to Prague?

stay in frankfurt and berlin as your home base. from there you could visit dusseldorf, and koln, or mainz. from berlin you could visit leipzig,dresden, or hamburg.

If I remember right, Dresden is only about 2 hours from Berlin by train, and Prague is about another 4 hours from Dresden. You can check the DB website.

"Could we see Dresden in a day then on to Prague?"

There are Eurocity (EC) trains leaving Berlin every 2 hours from 6:35. The trip to Prague's Holesovice station takes about 4¾ hours with a stop half way in Dresden. So, if you left Berlin Hbf at 8:35, you would get to Dresden at 10:52. You could spend four hours in Dresden, leave Dresden at 15:10, and get into Prague at 17:18 (5:18 PM). If you wanted to spend 6 hours in Dresden you would have to either leave Berlin at 6:35 or get into Prague at 7:18 PM.

I do NOT recommend driving from Berlin to Prague in one day. In shear mileage it is certainly possible. However, in order to travel that far in one day, you will have to stay on the main highways, and, therefore, miss visiting several of the best places to see in that part of Germany.

So here's at least one alternative: Leave Berlin first thing in the morning, and head south to the city of Leipzig - easy to get to right down the Autobahn. In 3-4 hours, you can comfortably visit several of the key sights in the historic downtown area of this city - St. Thomas church, where Bach was choirmaster, the Nikolai Kirche, where the quest for German reunification took hold, the opera house, the Auerbachskeller from Goethe's Faust, etc. ... enough to at least get a feel for the city. You can then leave Leipzig, and drive southeast toward Dresden by mid afternoon .... but go only as far as Meissen. It is small, but the Albrechtsburg is worth a visit. Stay the night in Meissen, and then head for Dresden early the next day. Dresden in definitely worth the bulk of a day - you can visit the Zwinger, the Frauenkirche, etc. By mid-afternoon you could then head south to Prague, and be there in time for an evening meal.

Check out Kitzingen and Wuerzburg if you want to see Bavaria but skip Munich. Wuerzburg has the Residenz which is a UNESCO world heritage site and Kitzingen is just a nice little city. Also, several smaller towns in the vicinity - Iphofen, Dettelbach, and my favourite, Mainstockheim, because we have family and friends there. All have festivals at various times, mostly relating to wine.