I kinda like Ken's website, as he often posts up interesting articles. From a scientific point of view though, this comparison is among the worst I've ever seen. At the very least he should have used a top canon lens, and not one that's known for lack of corner sharpness when shot too open.
I think the only possible way to make a review like this is shoot both cameras with the same lens. This would HAVE to be a sharp and preferably calibrated (for each body) 3rd party lens. Another option would be to at least use one of the best known lenses for each camera, so not the 50/1.4.
Another note: shoot with the same aperture, iso speed (unless one camera offers a lower value). do NOT use jpeg. Just... don't. The way this review is set up, Ken Rockwell appears to intentionally make the Canon 5DII look bad. I have no trouble believing that the D3x is better than the 5DII, but this review would be unacceptable even for first-year students. There's just too many variables left unclear, uncomparable or just plain wrong.
I hope Ken accepts this critique and fixes his review by revealing ALL the testing parameters and not just stating additional tests showed the same results. This is just condescending and making a mockery of people who are interested in the actual differences and whichever one wins - by what margin it does that.