Independent bookstores face increasing financial pressure from the rising use of ebooks. Amazon offers many ebooks at a significant discount. This makes it tempting for frugal readers to buy there, especially if they own a Kindle (which device itself is sold at a loss to entice owners to buy their ebooks from Amazon). But there are other options which support indie bookstores and authors directly.
Currently (July 2012) IndieBound.org (a community-oriented movement begun by the independent bookseller members of the American Booksellers Association) member bookstores will sell you Google ebooks though their bookstores’ websites, which gives the store you choose some share of what you pay. You can read Google ebooks with the Indiebound reader app for Android and iOS, with Google’s Play app, with Adobe Digital Editions software on Nook, Kobe, etc, and can be side-loaded onto Kindle. Find links to independent bookstores selling Google ebooks here.
Unfortunately Google has decided to stop the bookstore reseller program in January 2013. But keep an eye on IndieBound.org for a replacement program.
A number of publishers sell ebooks directly from their sites. since I read a lof of SF, one of which I know is Baen. They also have an awesome FREE library of some of their older titles and 1st titles in a series. MacMillian will also sell your their ebooks.
Check the author’s website, as more are choosing to self-publish and self-distribute. And if you buy directly from the author more of the money actually goes to him/her since they don’t need to split it with a distributor.