I knew I could trust Samsungian to do the cost analysis for me, so I'll focus on usability and other issues. He always saves me work
When I decided to go FF, I had some very clear objectives. First was good hi iso as I shoot low available light a lot. Second was the ability to crop and still print large. Unfortunately those both favor different choices (D700 for first, 5D2 for the second).
So, then it comes down to individual choice. Ergonomics are important to me, and I hand carry for long periods so the body has to feel right in my hands. I found that the D700 to feel more solid, but there is a ridge in the finger tip area that I don't really like. Some aspects of the buttons and menus I don't care for on the D700, but nobody gets this perfect. I wasn't a fan of Canon's approach at first.
I shot both the D700 and 5D2 a couple of times at my local shop along with my K20d for comparison. I then took the files home and pixel peeped to my hearts content, and performed some of what would be typical PP.
Then you have to consider what glass you're likely to want to shoot. With Pentax I liked fast primes, but frankly neither Cannon or Nikon has anything like the ltd primes. But by contrast some of their zooms are pretty amazing, and there are some incredible primes as well. They are just bigger and more expensive (some) than Pentax. I wanted IS/VR in as many lenses as I could get as I'm used to it and shoot handheld/low light a lot. This was where Canon won imho. The "kit" 24-105/4IS is way better than the Nikon "walkaround zoom." For the 24-70, neither have IS, and the Nikon is about $500 more. Nikon also doesn't have anything like the 70-200/4 IS (relatively small/light but high quality longer zoom - like the 50-135*).
In the end, having the 5D2 feel better in my hand and the glass choices for what I wanted tipped the scales towards Canon. After I bought it I wondered if I would have been better off with the D700 which does have about an extra stop of hi iso performance and "better" AF for tracking, etc. But I don't really shoot tracking stuff, instead used to single/center point. If you read the forums, some people claim the 5D2 has "terrible" AF, and rail against Canon for it. In my experience, it is just another example of forum whining by most of the users. The extra MP of the 5D2 help a lot with cropping, and also help to equalize the hi iso issues. I can shoot 3200 without worrying, and 6400 works in a pinch.
Right now I have a few L lenses that cover most everything: 16-35/2.8L II, 24-105/4L IS, 70-200/4L IS, 135/2L, and a 50/1.4 that was under $400. Not thrilled with the 50 but it is ok for the money. The 70-200/4L IS is worth the price of admission imho...stellar lens.