No comments, huh?
My vote would go to the Nikon D3 for detail retention at ISO 3200, 6400 if you need ISO speeds that high. It's full frame, Nikon designed 12MP sensor is hard to beat right now for that purpose.
It's AF system is pretty good, too (with sophisticated algorithms that even take subject color into consideration while tracking). But, keep angle of view differences in mind going to a full frame sensor (no more crop factor/focal length multiplier for angle of view differences like you'd have with an APS-C size sensor).
In the Canon lineup, I'd look at 1 series bodies for their best AF systems.