Salzburg is full of high-end restaurants. The current issue of Gault Millau Austria (www.gaultmillau.at) lists 20 restaurants with at least one toque.
The three toque places are:
I never miss the Pfefferschiff when in Salzburg ...
If you enjoy game, particularly venison, Goldener Hirsch is a great place for it. They also have wonderful Salzburger Nockerln for dessert. Some will say it is touristy, being in a hotel in the center of the old town, but there is no denying the quality, and the service is warm and attentive.