Faster! Not only is the frame rate much faster, the D3 is way faster than the D300 because it has bigger motors, bigger AF-S drivers and more processing horsepower to do all the math required of the AF system. I suspect the D3 will similarly be faster than the D700.
5:4 crop mode (not in D700). I use this daily!
D3 has onboard live backup with a second card slot, which I use all the time. D700, as an amateur camera, only has one slot.
No sensor cleaner working every time you turn it on means the D3 probably fires up faster than the D700.
Bigger battery, unless you add the grip to the D700.
D3 has a rear data LCD, which I've not found that useful. D700 has none.
Shutter "tested" to 300,000 cycles, vs. 150,000.
Better finder for DX; the D3 crops well instead of just drawing a rectangle.
D3 may have far superior finder if the D700 has the same silly obstructive-black active AF area indicators. (The D3 has unconstructively lit active AF areas.)
The D700 has no card-door release lever, since the new INFO button is there. I suspect the D700 card door will feel worthless and weak, like the doors on my Canon DSLRs.
The D700 is an amateur camera. By default, the D700 has the idiot beeper (CFN d1) ON, while the professional D3 has it OFF.
The D3 is tougher.
The D3 has a super easy-to-use note-taking function: just press the mic button