Earlier today, Gizmodo pronounced the $9.99 eBook dead, as a result of an announcement by Hachette that it is joining Macmillan (and probably HarperCollins) in instituting an agency pricing model where resellers such as Amazon and Apple will get a 30% commission on sales of eBooks at prices set by the publishers themselves. (I've learned from a source that Penguin is working on its own agency plan to be announced in a few months.) Of the Big 6 trade publishers, only Random House and Simon & Schuster would be without an agency model for sales of eBooks.
In response, Amazon has a number of tactics that it can execute. First, it can limit distribution of print titles from publishers who impose agency deals. The "nuclear option" that Amazon exercised against Macmillan backfired because the company "capitulated" almost immediately. However, a longer-term strategy of purchasing fewer print copies of Macmillan's titles, letting them go out of stock more often and taking longer to refill inventories would serve the same purpose. If the eBooks are available day-and-date with print versions and in unlimited quantities, while the print versions are often out of stock, it would provide more incentive for readers to move to eBooks.
Amazon could also play one publisher against the other, offering more promotional support and even co-op funds to help pay for newspaper, magazine and television advertising, in return for more pricing flexibility. Those publishers who cooperate would increase their revenues and/or decrease their costs, and would put pressure on other publishers to fall in line.
Finally, I expect Amazon to get even more aggressive in pursuing electronic rights from established authors. Many established authors or their estates have contracts with publishers that predate the eBook era, so they retain their eBook rights. There is a strong body of legal precedents and settlements that favor the authors and estates in cases where their print publishers claimed eBook rights that they had not specifically been granted. Amazon can price these titles at $9.99 or less and still offer extremely attractive financial deals to authors.
In short, the $9.99 eBook is far from dead, and Amazon still has many ways to prevail in the long term.