Nikon often seems to have the edge in body development. Better flash metering, better AF at a given body price point (though it's debatable whether anything beats whatever the current Canon 1D is). Nikon did a great thing when they released the D700 full frame with only 12MP. Everyone, including Canon, is caught up in the megapixel race. I almost never wish for more megapixels from my 40D but I sure would fancy a usable ISO25000 mode sometimes.
When I bought my first DSLR (a Rebel XT) I was buying into the SYSTEM, and not just the body. Generally, it is easier to get better lenses for less money shooting Canon. My entire photo kit is second-hand, bought via forum buy and sell. There's more Canon stuff out there, so there's more for sale. All of my glass is L glass and it all performs very well (which is not to say that Nikon doesn't make some great glass too).
If I was starting all over again, I might go with Nikon, but I have no dissatisfaction with Canon that warrants dumping the whole system.
