1. Technically, the USPTO hasn't yet "invalidated" the patent; it issued a first "Office action" in which it stated that all of the patents claims were unpatentable in view of varying combinations of prior-art references.
2. Institutionally the USPTO is very much aware of the significance of reexamination for a patent in litigation.
3. The Office action was signed by a "primary" examiner, i.e., someone who has been around the block a few times. Another primary examiner and a supervisory primary examiner are listed as "conferees." You would be right to read this as a signal that the USPTO takes these matters very seriously; the detailed written analysis (which I haven't studied) seems to bear this out.
4. The primary reference cited is a patent [1] filed in November 2005 whose lead inventor was Danny Hillis --- dare I say, the legendary Danny Hillis [2].
Another main reference is a Japanese patent publication from 2000, referred to as the Nomura reference.
5. In responding to the rejection, Apple can try to establish that their inventors predated Hillis's November 2005 filing date. This is referred to as "swearing behind" the Hillis patent's filing date [3]. But the Apple inventors' filing date is January 2007; swearing behind that far would be a real challenge. (I won't go into the details of the statute and regulation unless people are interested.)
Apple can't swear behind the 2000 Nomura publication because it was published more than one year before Apple's January 2007 filing date --- see 35 USC 102(b).
6. Paragraph 14 on page 34 is pretty typical: It says, in effect, "you'd better take your best shot at contesting this rejection now, Apple, because the next time around it will be a final rejection."
7. If, as seems likely, the USPTO does issue a final rejection, Apple can appeal, first to an administrative appellate body in the USPTO, and if necessary to the U.S. Court of Appeals for the Federal Circuit. The Federal Circuit is required by Supreme Court precedent to be fairly deferential to the USPTO's findings in some respects, but it's not entirely clear to me how that would play out here.
[EDITED FOR STYLE]
[1] http://www.google.com/patents/US7724242