I have a Canon 20D and Canon 24-70 f/2.8L and a Nikon D700 and Nikon 24-70 f/2.8.
Here's my take on the two systems for what I use:
1. Both the Canon and Nikon versions of the 24-70 are excellent, but the Nikon is definitely sharper wide open. Nikon lenses also have a 5 year warranty vs 1 year for Canon. I've never had a Canon or Nikon camera or lens in for service though so not sure what the extra warranty is really worth 
2. While I've owned a 580EX II and it was fantastic, the SB900 is a better flash due to having much better menus. The flash also comes in the box with a diffuser and gels which is a nice touch, although IMO isn't worth a premium.
3. Setting up multiple off-camera flash units using iTTL with the D700 is much easier than with my Canon system. Being able to use the popup flash as a commander has really been useful for me.
4. IMO the D700 is a much better general purpose shooter than the 5D MKII due to it's pro AF system.
5. The higher fps of the D700 comes in handy when I shoot at my daughter's swim meets.
6. For what I print the higher MP of the 5D MKII would rarely be useful, but I can see how some would need it. As a test I printed a 16x20 from my D700 and was very pleased with the results. 8x10 would more typically be the max size I print though.
7. I was pleased to see that Nikon has a pretty inexpensive wireless remote for the D700. Works fine.
8. I don't have any issues with either the Canon or Nikon control layout or menus. You can easily get used to both.
9. The Canon battery charger is much nicer than Nikon's (stupid cord) 
I also have a Nikon 70-200 f/2.8VR and a 70-300VR (for a lighter carry-around lens). The 70-200 is a very nice lens but does vignette a bit more than the Canon equivalent. The excellent IQ from the consumer 70-300VR was a pleasant surprise.
All in all if the 5D MKII came out with an AF system closer to the 1D series I would never have bought the D700. If you don't need the high resolution of the 5d MKII or the AF and fps of the D700 then either camera would be an excellent choice.