A number of people, including the owner of this forum, have suggested that the Nikon is a high-ISO offering, to be supplemented by a high-res version of the D3 sometime next year, maybe even in the Spring. That is, comparing the D3 to the 1Ds3 may not be apples-to-apples.
In most cases, in careful printing, I doubt you'd see much difference at 16x20 between the two, simply because the print isn't large enough to really express it well. But any larger than that, assuming that both cameras are being shot in their sweet spots, under similar conditions, I don't think a 12mp Nikon could compete with the resolution of a 21mp Canon. All of this, of course, is confused by the question of glass -- Michael Reichmann suggested a year or so ago (too lazy to look it up) that using Zeiss glass on a Canon (with adapters) made a significant difference in image quality -- which suggests that the Canon lenses he used were not everything they could be. If the Canon glass also falls short of Nikon glass, then, who knows what the extra res would do? Should note that Zeiss makes a line of ZF lenses, which are prime lenses in a Nikon mount, and which, I am told, offer some pretty astonishing results when mounted on a D3.