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!