Well, as Aaron alluded to, there almost certainly ARE true co-integrating relationships out there, but if you don't look for them with the thesis first, they are drowned by all the false positives caused by spurious relationships. In the same way that http://rnm.simon.rochester.edu/research/FMFM.pdf points out that momentum might be basically about earnings momentum, perhaps the solution is to choose a narrow basket of stocks with known co-integration to some external/fundamental driver(s), then trade the residuals of those predictions. Instead of trading four refining stocks against each other, trade four refining stocks against their predictions based on their relationships to oil price, oil contango, crack spreads, natural gas, who knows...
I don't know much about the underlying rationale of this model http://www.tradingvolatility.net/p/spy-arbitrage-model.html but the idea is interesting, somewhat unrelated.