First off, I encourage everyone to read the actual paper at http://arxiv.org/pdf/1110.2685v1 [PDF], I think many here are seriously overestimating the complexity of the author's claim.
I've mostly said this already on this thread, but it's buried near the bottom of the page, so I'll summarize the paper here, it's extremely simple:
0) If you're measuring time in the reference frame of the moving clock, you've got to transform the length between the stations in accord with the Lorentz transformation. According to this author CERN already did this, so it's entirely irrelevant to the discussion - I couldn't verify this, because it's not mentioned in the CERN paper he referenced.
1) What they did not do (according to this paper) is account for the fact that in the satellite frame, during the neutrino's flight the receiver station was moving towards the source.
2) time = distance / rate
3) CERN used rate = c, but they should have used rate = c + v because the receiver station was moving towards the neutrino.
That is quite literally the entire thing, check the math in the paper if you don't believe me. This is not a claim that CERN somehow misapplied special relativity, it's a claim that they simply forgot to include the motion of the receiver.
IMO this is far too elementary a mistake to have been missed for this long, so I'm suspicious. The CERN paper that the author references (http://arxiv.org/pdf/1109.4897v1) doesn't discuss relativistic corrections at all, so I don't know why the author assumes this mistake has been made, perhaps he's reading another paper that he didn't reference? From the OPERA one that he links (though I haven't read it in too much detail) I get the sense that if it was this simple, one of the many calibration tests that they've done would have easily caught the error (they talk about a lot of bidirectional synchronization stuff), so for now, at least, I would take this with a grain of salt.