Good additional points. Unfortunately, I cannot edit the OP to add to my table...maybe a new thread if there's enough interest.
I wonder how many people make use of the microphone/voice recording feature of the D3? I've never made a voice annotation on my D2X.
The built-in commander flash is a nice feature. I've used that a number of times with my D300, although I prefer the SU800 because to make changes with the built-in flash you need to go into the menus, which is cumbersome. You can do the same with an on-camera SB800, but I don't usually do that because the SU800 is lighter and smaller.
Now that the D900 and D3X are being rumored, with most folks thinking of the D3X as a certainty, what to buy....???