If I only have time to visit one, which should it be? We enjoy flea markets, great scenery, and browsing through antique and junk shops. This will be a spring or summer visit.

This might not be the reply you want, but I would recommend you spend more time in Munich and see Salzburg as a day trip from Munich. Unless you want to be included in a lot of touristy/kitschy stuff you'll find much more of interest in Munich. I spend two days in Salzburg and after one day wished I had been in Munich instead. (If I ever see another Mozart ball again I'm going to scream.)

Completely agree with previous post. If you must choose, choose Salzburg unless you're an Olympic skier.

Im going to both, though spending 2 nights in Innsbruck and overnight in Salzburg. its hard for me to skip any one of these 2, so i've decided to save a bit more but leave for europe a few more weeks later. that way i don't miss any of the places i've been dreaming to see. hope this helps.

Hmmm.. I find it interesting that two replies suggested skipping Salzburg and Innsbruck. I have been to Munich a couple of times and just travelled in Austria and I loved Salzburg and Innsbruck! I would choose Salzburg as my favorite out of the two.

Maybe I'm in the minority, but I liked both Salzburg and Innsbruck more than Munich (although I liked Munich, too).

If I had to choose one, I'd pick Salzburg because it seemed so quaint when I was there. Although I loved Innsbruck, as well, it seemed more urban than Salzburg.

Good luck with your decision.