Here I will give you a rundown of papers that have made it to pre-print which point out these errors.  Much will be written about CERN’s latest numbers, allot of it will not spend much time on “systematic errors”, here are a few examples.   CERN's setup having systematic errors is not what makes them wrong, that they did not recognize these things does.

One of the things every scientist learns is that the most pernicious, most hard to eliminate errors are systematic errors.  These are errors that exist because of the very setup of one’s experiment.  They can be hard to recognize, and hard to reconcile. Unless what you are measuring is a well-known property which has been measured a bazillion times before.  In those cases a finding of  g= 20 m/s^2 (on earth at sea level), or that Alpha centauri is only 0.4 light years away, or that neutrino’s fly faster than light needs to be adjusted after the fact to fit what literally millions of other scientist have found.   The logic being that any errors in all of those experiments will have canceled each other out.

Competent and even great scientist are wrong every day, the great ones figure it out before the press conference.  CERN's team is certainly competent.

This is not just the musing of one random person.  Here is a list of papers , not exhaustive, which points out the systematic errors in CERN’s Neutrino result.

These papers point out that CERN's results rest on certain assumptions about the neutrino beam’s departure time and characteristics at departure.  If their assumptions are in error then their results are wrong. This is not an exhaustive list by any means.

“Possible systematic error in OPERA neutrino experiment.”  Edwin Norbeck and F. Duane Ingram, University of Iowa

http://cdsweb.cern.ch/record/1389521/files/CERN-OPEN-2011-042.pdf

“Possible Origin Of The Neutrino Speed Anomaly Reported By OPERA” Shlomo Dado, Arnon Dar

http://arxiv.org/abs/1110.6408

The following papers point out that CERN has likely made a timing error in a way that even their latest rerun of the experiment does not eliminate  , a systematic timing error. 

“Inconsistence of super-luminal Opera neutrino speed with SN1987A neutrinos burst and withflavor neutrino mixing” D. Fargion, D. D'Armiento

http://arxiv.org/abs/1109.5368

The above paper is most damming. This deals with a scenario where light and neutrinos were released from an event at the same time by a supernova. The timing of the arrival of the neutrinos and the light was consistent with c being the limiting speed (in essentially flat space-time which is close enough to Special Relativity’s unaccelerated reference frames for a valid comparison.)  This observation involves actual light, and actual neutrinos traveling through the same backgrounds and measuring their arrival times.  If CERN was correct, then the neutrino’s would have arrived YEARS earlier!   No such spike in neutrinos has been found in the archived data from that period.  Any theory which seeks to explain CERN’s result needs to reckon with the astronomical data on SN1987A .

 

These are just the papers I was able to find from a quick Googleing which deal with systematic errors CERN’s setup.  There are other objections both theoretical and experimental.  The most fundamental of which are listed here. 

I should also mention this one.  It sort of straddles the border between experimental systematics and theoretical concerns.   "Time-of-flight between a Source and a Detector observed from a Satellite" Ronald A.J. van Elburg  http://arxiv.org/abs/1110.2685

"Common-View Mode Synchronization as a source of error in Measurement of Time of Flight of neutrinos at the CERN-LNGS experiment" Satish Ramakrishna (_http://arxiv.org/abs/1111.1922) gives a more detailed account of  the kind of error CERN seems to have made which shorter pulses of neutrinos would not correct for.

In reading CERN’s papers I am reminded of these words from the great Richard P Feynman “The first principle is that you must not fool yourself and you are the easiest person to fool.”  The scientist at CERN are all very distinguished and good at what they do, and should step back and consider that to confirm their result they may need a fundamentally different setup than what they have now.    

A space based experiment that would truly settle this once and for all. 

An experiment which mimics the supernova in that it releases both neutrino’s and photons at the same time, so we can see light and neutrino’s travel the same track, and see which one wins the race.  The only way I can see doing such a thing, would be with a neutrino experiment based in space, and the detectors here on Earth.  With the neutrino and the photon leaving at known times, and traveling through the same conditions all the unknowns inherent in a setup like CERN's would be eliminated.

A satellite with a neutrino source could be placed in geosychronous orbit over a selected point on Earth's equator.  The distance   to geosynchronous orbit is well known, and much larger than the 700 odd Km that CERN has to play with.  Any difference in the time of flight of the neutrino and photon packets would be magnified by this distance.  The result would be clear and convincing to all.  

While the technical details of such an undertaking would be a challenge it can be done.   

Corrected for minor punctuation errors.  Any comment that in future is not about physics will be deleted. 

Update: 2/25/2012
It seems I was right about them being wrong... the whole thing was caused by a loose wire. 

New Theory on that Faster-Than-Light Particle: A Loose Wire