Hmm, good question!
I like a simple site. No flash or other newfangled things.
I should be able to search for an author, first name, last name, combination, title of the book or keywords (as a minimum)
I also need to be able to narrow my search by format and if I don't, all available formats should be visible.
The details of a book should at least have a cover, price, available formats, author, title (etc) and either a short excerpt, or even better, a preview download (one for each format).
PayPal should be available as means of payment.
The bookshelf should have a tree-structure, with at least 4 levels. You decide how that tree is built up. It should show you the date you bought the book and the format(s). Covers should be available but you should be given a choice whether you want to see them or not. And you should be able to filter your bookshelf by format, independent on how your tree is built up.
Format, pricing, geographic restrictions are generally things not dictated by the shop, I won't comment on those, though I prefer a multi-format, low pricing and no geographic restrictions, but that is logical and doesn't need repeating.