First, everyone needs to listen to this podcast from SF Signal, featuring a round table discussion with Alan Beatts (owner of independent bookstore Borderlands Books), Chris Roberson and Alison Baker (owners of publisher Monkeybrain Books) and author Cat Valente. The subject is "What the Borders Bankruptcy Means for Brick and Mortar Bookstores" and the discussion is something everyone concerned about the health, quality, and diversity of literature should hear.
Then you need to go to this post on the blog Reluctant Habits, where Edward Champion has posted an invaluable List of Independent Alternatives to Closed Borders Bookstores. This is a list of all the Borders stores being closed and independent stores nearby (with their proximity in miles).
Then put 2 and 2 together.