I've owned both systems. So far a Nikon D50, D200 and a Canon 5D Mark 1. I bought the 5D because it was cheaper for me to buy used then a used D700, and I needed full frame for tilt-shift lenses. The biggest downside to Nikon for me is they don't have a 20+ MP semi-pro body (yet). If you need a big sensor (printing large landscapes for instance) you need to cough up $5k+ for a D3x.
Outside of that however, I prefer Nikon. The AF system was much better (even my D50 had a much faster/more accurate AF system); in response to the poster above, my D50 with a screwdriver 80-200 was faster/more accurate then my 5D with a 50mm f/1.4. The D200 was even faster. Additionally I had a lot more control over how the AF system worked.
The build of the 5D is similar to my old entry-level D50, the D200's build was much more substantial. From a UI perspective my Nikon's were much more intuitive to use, although I do like Canon's implementation of the little joy-stick better then Nikon's larger D-pad on the D200 which is too easy to accidentally hit with your face. My Nikon's gave me much more control over all sorts of settings, and had dedicated buttons on the body for each function that were easy to use when looking through the viewfinder. Canon's overloaded button system with non-ergo placement isn't nearly as friendly for me.
Anyways, I recently bought a 4x5 for landscape, so once the price on used D700s comes down I'll probably go back to Nikon (I've gotten way to used to the benefits of FF to go back to crop sensors).