In today's camera market, the ergonomics of the camera body itself are the largest differentiating factor. Nikon and Canon have *very* different control systems for the most commonly-used controls over lens f/stop, shutter speed, and the assigning of the AF point. At the D300s and 7D levels, which is variously defined as the low-end pro/pro-back-up/high-end prosumer model/or semi-pro body class (whew!), the MAIN differentiation is the way the camera's user interface is designed, thought out, and actually built.
As far as KmH's assertion that the image quality is the #1 criteria, I disagree with that statement: to me, the camera's ergonomics and its control systems are the MAIN points of interface between me,and the camera. The image quality nowadays is more than comparable between cameras within the same class; I have Nikon and Canon bodies and lenses and flashes. TO me, one of the systems has a much better, more control-driven interface,with a better system,especially as far as adjusting shutter speed and aperture and selecting the focusing point in use, and the AF modes, as well as the AF-On and AE-Lock button system.
Some people prefer Canon's menu-driven and dual-purpose controls. Other people prefer Nikon's body controls and ethos. The two systems are actually quite different,and the cameras actually "handle" and "work" very differently in actual, real-world, day-to-day situations. This is based upon very different corporate design philosophies that go back to the mid-1980's,and which have not changed very much. Many users prefer one company's handling and operation over the other company's approach. The image quality is,to me, more than adequate for almost any use, whether it;'s a new Canon or a new Nikon.