I am surprised that Daring Fireball is the only one covering this story out of my wide ranging set of sources. According to the article linked, Amazon made some amendments a year into the four year re-examination process that have resulted in the patent being upheld. Those amendments arguably narrowed the patent’s scope though pinning it on a “shopping cart model”. This still seems overly broad. What e-commerce site doesn’t use a shopping cart?
There are two silver linings. The Bilski case currently before the Supreme Court could lead to an invalidation depending on the outcome. The patent expires in 2017 having been filed deep within the bubble in the nineties.