for Guitars, I think the three that I think have the best stock are:
1. Guitar Resurrection on Guadalupe (shares the same parking lot as Ray's Steakhouse) -- a lot of high end stuff like Bogner amps.
2. South Austin Music on south Lamar -- Great selection, cool people
3. Austin Vintage Guitars on south Lamar -- haven't been there in a while but they had some great old stuff last time I was there.
if you want a wider range of instruments I think you want to go to Strait.