Remember that 'glitch' back in late January where all authorhouse 'buy links' on Amazon went missing? Takes on a rather different meaning in the light of recent events, don't you think? (As a recent comment on that post brought to my attention).
I just tried out my first purchase with Powells online. It was pretty straightforward. It lacks a little of the functionality and coverage of Amazon.com but I can live with it.
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You mentioned the past issue that affected iU and AH books. I bet there is a good chance that, one way or the other, the issue has already been settled from the corporate standpoint. One way to test this would be to order an iU book from several sources and see where it is shipped from. Remember that Amazon and iU reported that they had entered a special agreement with Amazon a while back that allows Amazon to display iU books as in stock without having to pay for them until they are ordered by the customer. Previous to that time, Amazon ordered from Ingram and paid for the books prior to selling them to a customer. This basically allowed Amazon to not pay for an iU book until Amazon had sold it. Now the iU author gets paid later for the retail sale, rather than earlier for the wholesale sale, and any iU author can track this change with his or her sales and royalty account posted by iU.
I've been a fan of addall.com lately, and still source abebooks from time to time.
burkesbooks.com, and indie in Memphis, is a good one I try to throw business too as well.