I would disagree with AF currently being in favor of Nikon in general. In my playing around with Nikon DSLR bodies at the local camera place, I've noticed Nikon AF systems have very low frame spread. Particularly on the full-frame bodies. Most of their latest AF systems seem to be reticular, but the points are so tightly clustered around the center of the frame and so tightly spaced, I wonder if they are as broadly flexible as Canon AF systems.
In most, if not all (6D AF system yet to be seen, although I suspect it is the same) current Canon DSLR's, they support fairly broad AF point spread in a highly configurable setup, including the 7D, 5D III and 1D X (and even the 1D IV in a form). The new Canon 61pt AF system, used in both the 1D X and 5D III, has more total points as well as more cross-type points than any other AF system yet on the market. All of Canon's AF systems support a variety of selectable point modes, including Spot AF, Single Point AF, Expansion AF, and Zone AF (the 1D IV supports some of those, in a more tedious fashion with custom functions). This is in addition to the ubiquitous Full AF mode where all points are automatically selected. Canon AF precision is also improved for wide lenses, such as f/4 and f/2.8 aperture when used...which can be a huge bonus for f/4 L II supertelephoto or f/2.8 L II telephoto lens users. Canon was also the first to provide orientation-linked AF points.
I think some of these features found their way into the improved 51pt AF system used in the D4 and D800, however most of Nikon's AF systems only support dynamic AF areas around the center point (if they support a dynamic AF area at all). However, to my knowledge, Nikon AF points only have two levels of sensitivity...normal sensitivity for f/5.6 and lower sensitivity for f/8...so no bonus performance or precision to f/4 and f/2.8 telephoto lens users. I don't think there is any question that previously, when Nikon first introduced their 51 and 39 point AF systems in the previous generation of Cameras, they were generally better than Canon's (particularly the 1D III's botched AF system).
However at the current time, I think Canon definitely holds the AF crown...assuming were talking about who has the best of the latest and greatest technology (which is what I assumed before.)