Photoeye books is great if you're looking for something no one else has. Although their prices are close to retail, their prices on the Web are usually discounted a little and they do have sale books at a bargain. Over the past year or so, they've managed to locate a couple of out-of-print books I could not obtain elsewhere at a reasonable price. Used copies of one of the books was selling for over $200 but Photoeye obtained a new, plastic wrapped first edition for the original retail price of $45.
Otherwise, I buy a lot of books from Amazon's "new and used" merchants. There can be some great bargains through these sellers and I've never been disappointed in the service or condition of anything I've bought from them.
I usually just buy from Amazon; I like the convience. I just bought myself a copy of Jack Dykinga's "Arizona" (recently published) and am looking forward to seeing it delivered today (I used to live in AZ, and sometimes miss it).
Try Alibris.com. It is a book finding site that works through hundreds of independent new and used book stores to find titles. Rates the stores, lists available books by prices and condition. There are a couple of other sites like it but don't recall the names. I have been extemely pleased with purchases made and the condition of the books.