There has been a good deal of comment on recent goings on in the world of online book selling. I won't rehearse the arguments here but it you are interested then my colleague Jane made an excellent post on the subject on her blog, so excellent it was picked up by The Guardian as one of their Best of the Web items this week. You can read it here. She followed it up with this, which also makes interesting reading. The Scotsman also cover the story but from the perspective of new booksellers, and you can read that here.
So if you are looking for indie friendly alternatives to buy from online then here are a few:
For new books:
The Book Depository with its free world wide delivery is always a favourite.
Play.com sell new books plus some used books. They also sell games, gadgets, DVDs and such like.
For used, rare and out -of -print books:
ibooknet is a co-operative of British and Irish sellers of used books. The order process is a bit long winded but all the sellers contact details are available so you can fire off an email or telephone.
ukbookworld is only for books over £4 but this does mean that if you put in a keyword like Bronte you get decent editions and serious literary criticism or biography not pages and pages of tatty paperbacks of their novels. Like Ibooknet you can easily access the booksellers details to pay by phone or ask a question.
In North America there is Biblio who again make bookseller's details available and have a very fair commission structure which rewards the best behaved sellers.
Ebay needs little introduction in its various incarnations, and has both auction and shop style books for purchase.
Ebid, like Ebay has various national sites and this link lets you pick the nation closest to you via the drop down box at the top right. Ebid has both shops and auctions and is actually quite good for inexpensive fiction paperback and children's paperbacks.
Booksellers own websites: if you like the service a bookseller gives you google their name and see if they have their own website. Some booksellers include promotional material with a book but as many of the best know selling sites forbid this then your excellent knowledgeable seller might be too intimidated to let you know they have their own site. So have a look!
I hope the above is useful. It may save you from having to shop at the Other Place or its very many subsidiaries.
Edited to add: thank you for all the support on and offline. A few more links for you supplied by readers:
GreenMetropolis is an excellent venue for selling your own books within the UK with a clear and fair fee structure. They're also, hurrah, a site that recognises that some books cost more to post than others. 5p from each sale goes to the Woodland Trust. However they're not as cheap as buying from booksellers' own sites or from Ebid for cheap paperbacks, but they're still very reasonable.
Indiebound helps you find your independent used bookshop with in the USA
Quidco is a cashback co-operative. There's a five pound fee but only if you earn at least five pounds and you can get cashback for books, dvds etc bought from play.com and Waterstones if you click through from your Quidco members page.
Lastly someone pointed out that LOVEFiLM also sells films as well as rents them.