Brad Stone of the NYTimes just reported that Amazon has pulled Macmillan books as a response to a dispute over ebook prices. I can't confirm why this happened, but I can say that there are a startlingly large number of Macmillan titles that aren't being sold by Amazon.
I've glanced through the first 5 pages of books published by Tor Books (a Macmillan subsidiary). Most of the books are not being sold by Amazon; they're being sold by someone else. I've also looked at books published by other Macmillan subsidiaries such as Henry Holt, Roaring Book Press, FS&G, Metropolitan Books, St. Martin's Press, and Forge Books. Most of the books I checked are not being sold by Amazon anymore.
I have to say that I really think Brad is right. This is too widespread for it to be a coincidence. I agree that it looks like Amazon is retaliating in a price dispute.
I bet you're wondering why it matters who sells the book. Well, when Amazon sells an item it's eligible for combined or even free shipping. This applies even when a third party is contracted to handle the sale on Amazon's behalf. It's a sweetheart deal that makes the items covered by it a slightly better buy than those not.
And, Amazon controls such a large percentage of the book market in the US that this can actually hurt a publisher. Remember last year when Amazon threatened POD publishers? This is the threat Amazon held over their heads. One of those publishers responded with a lawsuit. It's that big of a deal.