There is a good post of 10 things epublishers should do for readers (the organic kind) by Jane at Dear Author (via Times Emit) - link These are all good suggestions, although one or two would be a matter of your personal approach (e.g. preferring PayPal, or wanting the ecom site to store your credit card details). The points about wishlist, gift certificates, downloads bookshelf etc. are true of any ecommerce site selling stock keeping units, tangible or otherwise - these are the elements of good interaction design. And the points about multiple formats, DRM, distribution (wide availability) are also well made.
The underlying point, of course, is make the customer experience better - more usable, more convenient, more efficient.
Have a look at the comments, as there is plenty of engagement with this post.