Sorry about not replying to you on the other thread a few days ago. I haven't been keeping up with HN regularly and forgot to check whether you had replied to my comment.
I think you are badly misinterpreting how the courts work. The Federal Circuit did not overrule Benson or Flook, even if Justice Stevens disliked their interpretation thereof in Diehr. Nor did the Supreme Court write off State Street or Appalat as bad precedent in the Bilski decision. When Bilski was before the Federal circuit, it rejected his claim and also narrowed its earlier criteria for patentability substantially. The Supreme Court affirmed the Federal Circuit's judgment that Bilski's business method was not patentable, but said that the extremely narrow 'machine or transformation' test identified by the Federal Circuit was too narrow, and would exclude many patentable inventions while seeking to exclude unpatentable ones.
Now, you're talking about this bit, I think: And nothing in today's opinion should be read as endorsing interpretations of § 101 that the Court of Appeals for the Federal Circuit has used in the past. See, e.g., State Street, 149 F.3d, at 1373; AT & T Corp., 172 F.3d, at 1357. (Bilski v. Kappos at 3231) Is this right? If not, ignore the following.
They're not saying those earlier decisions are bad precedent. They're warning people against interpretations of the form 'the enemy of my enemy is my friend.' You're reading it as a binary: they're not endorsing something, therefore they must be against it. but non-endorsement does not equate to condemnation. Their point is that they are not passing judgment on those earlier decisions at all, and it would be a mistake to look for an implicit endorsement of those decisions in the case they were judging at the time.
It's important to understand that courts don't like to settle open legal questions if they don't need to, and they definitely don't want to do it by expanding the scope on their inquiry. Why? Because that would put them on a collision course with Congress, and the judiciary is less powerful than Congress. The Courts could lose some of their existing powers if they exercised them too freely. So what a court much prefers to do when presented with a knotty problem (like the state of patent law) is to either throw the ball back into Congress's court, or to wait until a case comes to them where the issues are clear and well-defined. In the latter situation, the Court can make a straightforward argument that it is exercising its legitimate function of deciding the answer to a question that has been brought before it. The court does not want to look like it's asking questions of its own. So another way to read the non-endorsement statement above is 'don't anyone get the idea that we are trying to usurp Congress and articulate a new law here, because we're not.'