Realizing your post was quite some time ago, I've had my D1x for about a month now. I have been thoroughly floored by the quality of the images, and by the quality of the prints I get from one of the larger online services.
I've seen some odd behaviors here and there, the bright subject backlighting thing I read further down bit my wife one day as she took a picture of me, but Bibble was able to save it enough for a reduced online picture, but probably not really "production quality". It was a throwaway candid, but just the same, I wish it had turned out better.
I really truly wish that Capture 2 came with the camera. Being a software developer by day, I realize this is probably being outsourced to developers and sold to Nikon for them to resell with their name, or consultants are developing it for them, but I still feel they should include it with a piece of equipment of this sort instead of trying to make back their costs on the development.
My biggest problem so far is not really technical, but in the fact that the 1.5x multiplier turns my 28mm widest angle into nearly 40, making it hard to get inside-room shots. When I was looking for houses and toting around my Sony DSC-D700, I was able to get true 28mm shots, which even then were too narrow for some inside rooms. To get out to the < 28mm range, we'd have to pick up a lens in the range of 16-20mm, and they aren't cheap. That's probably the thing I miss most right now.