I have planned our 3 month Europe trip and think I have found some pretty good accommodation spots that are in the mid-range budget. I was very thorough with checking all online reviews I could find! For the towns you mentioned we are staying at the following -
We are staying at Haus Reichl in Salzburg which is a guesthouse I found online with fantastic reviews. We are paying 59 euro a night there for the 2 of us.
Berlin has the eTap hotel which I think (from memory) was around 50 euro a night, but we are staying at a bed and breakfast called the Itowe Gallery for 45 euro a night.
In Vienna we are staying at the Wombat Hostel in a private room for 58 euro a night. Apparenlty Vienna is supposed to have one of the better Wombat Hostels, though they are supposed to all be very good.
Hope that is helpful!