I love indie bookstores. Love them, love them, love them.
There are a lot of different ways to support your indie store in this tough economy. It's true that indie stores usually charge more than Amazon, but at an indie, or even a B&N, you don't have to pay for shipping, your books don't arrived damaged, and a trip to a cool shop immerses you in book culture. And where else will a bookseller ask you what you like to read, zero in on your likes and dislikes, then hand you a book you've never heard of, but end up loving? And I don't think I even need to mention all of the wonderful author events.
If you can't make it to your favorite bookstore, and if you have an ereader, think about purchasing ebooks from your indie bookseller. Most of them have gotten into the ebook business, and their prices are surprisingly competitive. So be sure to visit their websites before automatically going to that other place...
Don't know if there's an indie store near you? Check out IndieBound.