As for the comment up above about Canon costing less and Nikon having better glass or ergonomics, that is not necessarily true. Ergonimics have to do with how a person fits with the camera (or chair, or desk, or keyboard,...) and is person dependant. Better glass? They both make very high quality lenses and I would love to see facts supporting high end Nikon vs high end Canon giving different results in a professional shoot. For an purposes, they are the same.
As far as ergonomics are concerned, you are correct, I may have misspoken. It is entirely personal preference.
Apples to apples, Nikon is usually a bit more expensive. For example (an extreme case), the Canon 400/2.8 is ~$7100, while the Nikon 400/2.8 is ~$8900. Differences are less dramatic, but present, throughout most of the line. As far as the quality of glass is concerned, I can't site my source, but was told some time ago that Canon outsources production of glass (I believe to the same people Hoya uses, someone correct me if I'm wrong) while Nikon is completely in house. Regardless, of the MTF charts I've seen for the larger zooms, I recall the Nikon having the slight (albeit real world irrelevant) edge.
In the end, glass and money aside, the camera that is going to be best for you is the one you're more comfortable with. I think that's the most important thing.