I'm obsessed by noise. I want to shoot at high iso without noise (less possible). According to dpreview, they claim that "generally" nikon has lower noise levels that canon. But not by much - just like the tiny tiny details... Like I said, I'm obsessed. BUT, if you want more megapixels, then go with canon. They have 15 and 18mp at affordable prices.
Sometimes, It's just a matter of taste, weight, look and feel and what's available for accessorizing you cam. CHeers!