At this stage of the game, regardless of where one camera may excel over the other, both companies are producing outstanding cameras. Direct comparisons can be tough and for me, I always look at a piece of gear for what it is and what it does rather than how it looks next to something similar but with glaring differences...
I've shot both systems extensively and have a long list of likes and dislikes with each brand. I've been very frustrated and angered by each manufacturer and I've also been thrilled and completely in love with each, but I've come to understand that there is always compromise and no such thing as a perfect product.
Personal preference plays into the decision heavily. Some people like the ergonomics and controls of one or the feel of the body in hand. There are so many variables. Some want to pixel peep and analyze rather than just shooting, viewing and printing to determine if they like the IQ and color rendering. Auto focus and exposure systems vary and can influence your decision.
For many people, it's all about glass and while Nikon has a great selection of some amazing lenses, there is a general feeling amongst photographers that Canon has a more well rounded selection. I'm not saying it's true but it is the perception.
In the end, when viewing beautiful images, I can't tell the difference and don't care to look for them. Both systems produce stunning images and users are very happy. There will always be lemons and horror stories but those are usually isolated incidents and they happen on both sides of the fence.
My advice to anyone looking at DSLR bodies these days is to buy what you like and what makes you happy, even if it's something as silly as the logo or color, etc...
You can't go wrong with Nikon or Canon these days.
