Update: This possibility excluded by a new experiment with 3 ns pulses. I suppose an explanation along these lines would mean interesting new particle physics. However, the detectors were built to measure the oscillation, so I guess that the OPERA collaboration thought about it, and rejected it for whatever reason. Neutrino oscillation might, for example, then make early neutrino more detectable by the distant detector. It might be possible that the neutrino emitted early are not exactly the same as the one emitted late. The neutrinos are emitted on a 10.5 µs window, 175 times longer than the observed effect.
Update: Rumors seems to tell that the boring explanation is the good one. If this would however end up to be the explanation, it would be quite boring. The distance seems to be known within 20 cm and the synchronisation seems to be within 15 ns (6.9 statistical and 7.4 systematic). The arXiv paper studied them, and seem to exclude it. Of course, the current list only contains biases which are unlikely, but less unlikely than a causality violation. As many physicists (including, I guess, many people from the OPERA collaboration), I think it will end like the Pioneer anomaly. I thought it might be a good idea to list the possible systematic biases which could lead xkcd's character to win his bet. A high level description of the problem is given here and a more detailed explanation of the investigation is here. Last (?) Edit: The "problem" is solved: it was mainly a problem in the timing chain, due to a badly screwed optical fibre.
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