The D3 also has a more durable shutter, which is something that most don't remember. It's not a problem if one upgrades every couple of years, but if you plan to run it into the ground, a D3 will be more cost effective over time.
There are other things, too. Two AF processors, not one. Probably not a big deal for those who don't use stuff like 51-point group dynamic, but it is real in those configs.
More obvious are things like frame rate, buffer depth, etc.
Do I think it's worth it? Clearly I must have thought so, since I have a D3 rather than a D700.
_____ Brian... a bicoastal Nikonian and Team Member
My gallery is online. Comments and critique welcomed any time!