In Prague, we stayed at Hotel Pod Vezi (see separate review for this and others) and was there for 3 1/2 days, including the day we arrived on the redeye and the day we left. Overall we found Prague very, very crowded even when we went away from tourist spots. But people were friendly and eager to please.
The first day we checked out the Charles Bridge then relaxed in Kampa Park, finding great food stalls for dinner. The next day we saw the Jewish Quarter (I was touched by how much interest there was to see this, beautiful memorials and synagogues), the the Old Town Square, then relaxed in the Franciscan Park followed by a concert at the Clementium (nice choice) followed by sausage-y dinner at Kolkovna. Last full day we spent at the castle/cathedral - EXTREMELY crowded even though we were there early. The walked up to Petrin Hill and really enjoyed the observatory,rose gardens,and walk back down to the city.
The next day we were off to Vienna via train (bought tix two days earlier) with plans to stay for two nights. Vienna was beautiful with lots to do. After checking into Hotel Alstadt, We found a street fair and had some local snacks, then walked through Volkspark and off to Wratschko for dinner (yum!). We packed a lot into the next day, since we only had two nights in Vienna. The Vienna Museum (great for history and a Klimt retrospective) followed by a walk through the market (best doner kebab ever!) and then the Secession Museum for more Klimt, then a tour of the Opera House. Stopped at the Sacher Hotel for the mandatory torte, then shopped a bit en route to Stephens Church. Finished the day at the Medieval Jewish synagogue and excavation site. On our last day, we took the train (easy, clean) to Belvediere for great palace and art exhibits, then headed back to the hotel before going to the train to Budapest.
Arrived at Starlight Suiten (meh) for our four-night stay, then walked across the beautiful Chain Bridge and to Carne di Hall for dinner. Yum. The next day we saw Stephen's Basilica (wow!) then a tour of the Parliament (tip: get there early, if you have to wait, the Museum of Ethnography is mediocre, but the building it's in is awesome). Walked up the main shopping street Andrassy Way then my husband went to the Museum of Terror which he really appreciated historically while I walked up to the park at the end of Andrassy (People's Park?) and walked around beautiful grounds. We met for dinner in a lively square near Vorosmarty Metro. I should mention the Metro was easy to use and convenient.
The next day we walked up to the palace/castle which was o.k. The labyrinth caves were pretty cool, then we ran into a folklore festival at the fisherman's castle and at that point were "vacationed out." We took the train(s) up to the Buda Hills and had lunch up there, maybe should have spent more time in that area. Headed back to town and had a nice dinner at Paris Budapest.
For our last full day, we went to Margaret Island. We had a great time laying in the grass, walking around, visiting a few small things to see, and then swimming and lounging at the amazingly complete public pools - Palatinus Strand.
Before flying out on our final day, we visited the Great Market Hall then the synagogue. Good morning of touring before heading to the airport for our flights home.
Overall we enjoyed our trip. We'd have done one fewer day in Prague and one more in Vienna if we could do it over. (Maybe skip Prague if we were going for shorter). We'd have researched the Buda Hills better. Otherwise it was a really nice pace, plenty to do, easy to get around and figure things out.