So what happened was, the court did not comment on whether or not Congress was in recess. What they said was that any and all "intrasession" recess appointments are unconstitutional, only "intersession" recess appointments are allowed. Well, if that's true, then a whole lot of people will have to lose their jobs, because Presidents have been using doing this exact same thing for many years, including many of those appointments made by Clinton and Bush that jcb listed. And what's more, this exact legal question was decided in the President's favor back when Ted Kennedy challenged George W. Bush's nomination of William Pryor to the 11th Circuit:
http://www.wlf.org/upload/101404RS.pdf
So, why would this be constitutional when Bush does it, but not when Obama does it? Because that is what this court is saying. Again, they're not commenting on whether Congress was or was not in recess, at least not from what I've read about the case. They're trying to issue a sweeping ruling against ALL such appointments, and I'd just about bet this will get shot down by the Supreme Court.