21 days in Prague, Vienna, Budapest - Itinerary Suggestions?

Cesky Krumlov... overnite if possible. I spent two days there and could have stayed one more, but it was at the end of a trip so liked the slower pace.

I'll just quickly answer for the Budapest day trips. I think Pecs is too far for a day trip, especially if you like to be leisurely. I'd say head down from Budapest at a reasonable time in the morning, spend the night, and then return to Budapest in the late afternoon or early evening of the second day. I also think the Danube Bend is better done with an overnight in Visegrad, but if you had your own car you could probably run through all three cities in a single day. Think about opening times, though. If you start in Szentendre, the small shops and cafes that make it so charming won't be open early enough for you to enjoy them before you need to push on to the next city.
Can't say enough about how great the Wachau Valley is as a day trip from Vienna. We started in Melk with a tour of the Abbey and then did a 26 mile bike ride along the river and through the vineyards. Just fabulous.

RS Eastern Europe Guide Book covers all three of your cities.
You should get it if you do not already have it as it has lots of good information that we have used in the past when visiting that part of Europe including RS Eastern Europe Tour.

I guess I'm a little confused - the trip is 3 weeks long, but you have 9 days listed? Will you spend 7 days in each city? I agree with the above that Pecs and Cesky Krumlov are a bit far for day trips, based on the length of travel time involved each way.

Thanks so much, everyone, for your feedback. This is really helpful! The days indicated are for the base cities only. The side trips would be in addition to the number of days indicated.

I haven't done it myself, but Sopron looked like a good day trip from Vienna. I did go to Graz, which I liked very much, but I stayed there - it might be a bit far for a day trip. I'm hoping to visit Szeged on my upcoming trip for the Art Nouveau era architecture, but again, that may be too far for a day trip.

I went to Terezin while I was in Prague. It is very interesting. Unlike the other camps, the entire walled city was turned into a prison. This was the camp that the Red Cross and other foreign visitors were shown. The museums in the town give a very good idea, mainly through drawings by the internees, of what life was like. I haven't been to any of the other death camps so I can't compare.

We did 19 days in V, B, Split, Ljubljana, and Vienna. 4 days V - about right - did Melk-Krems which was great
DO NOT MISS THE HEURIGERN! 5 Days B - one day too long - went to the Opera (very reasonable), House of terror, Memorial park. Do not miss the roman ruins, which we did miss. We went to Eger, which was also fun. We went to Plitvice Lakes in Croatia - A MUST SEE DESTINATION. We also went to Split. While I enjoyed Split, it was a lot of driving. If I were you, I would consider Zagreb, Plitvice Lakes, Rovinj (Croatian coast)/Istria, Ljubljana (my favorite city of the ones we went to) and back to Vienna. You can do a circle tour - Prague-Vienna-Bratislava (3-4 hours is enough)-Budapest-Zagreb-Plitvice Lakes-Ljubljana-Salzburg-Vienna. You can also hit Mauthausen Concentration Camp, which is another must-see. I really enjoyed all these places. I'd love more time in Budapest, Ljubljana, Croatia in general.

Also in Budapest make sure to go to the Commie-themed pizza restaurant Marxim, at the N end of Castle hill on the Buda side.

The Holocaust Museum in Budapest, which is fairly new, is very impressive. And I loved the Post Office Museum - not what I expected.