"Thanks everyone for your suggestions. They are really helpful and I appreciate everyone taking the time. If you have any other information or suggestions about the Berlin, Prague and Vienna City Tour, please feel free to respond. Thanks again."
The Berlin, Prague, Vienna tour keeps you pretty busy moving every couple of days and packing in a lot of tours. You may be a bit worn out by the time you reach Vienna. I also think you are falling into a very American tourist syndrome of rushing about in an effort to see everything you possibly can.
My advice: slow down and enjoy Vienna. Linger over coffee and pastries in a cafe; visit Schonbrunn Palace and enjoy the garden and fountains; Visit the Albertina Art museum and linger over the paintings you like; find a concert or, if you are there on a Sunday, attend a choral mass at the Augustenian Chapel in the Hofburg Palace.
Finally, begin planning another trip to see the things you missed on this one :)