Hotels in Vienna and Salzburg are plentiful, but here are two that I have stayed at and had a good experience. In Vienna the Tourotel is good. It is part of a chain, but the location is good the staff is friendly, the rooms are good sized and the price is reasonable (60-70 EUR).

As for Salzburg, we have stayed at the Trumerstube. It is close to old town and the Meribell Gardens. It also has nice rooms and a pleasant staff. This one will run you about 100 EUR, but the the location is great.

Happy travels.

Greg