I find a fair bit of cool goth/punk clothing in thrift stores, I used to buy it on clearance at Hot Topic at the local mall, but in the last 7 years or so, the styles they stock in store have dramatically changed, so that now it is all Twilight shirts, and t-shirts with ironic statements on them.
Also, if you are into alternations and whatnot, lots of cool vintage thing from thrift stores can become the sort of style of clothes you are looking for. I talk to people at my local goth clubs, and either they make their own, buy cheap and alter, or buy at expensive online stores for the most part. I would ask around at your local goth clubs, usually there are some people who make things as a hobby that will give you a price not too much more than those boutique stores.
I also find the magazine Gothic Beauty is a pretty good source of finding stores, and about fashion in general.