After having used a Nikon D2X for almost three years and having cleaned its sensor on a regular basis without any problems (exactly as described in John Cotes post above), mostly usually before important shootings, I must say that I was shocked when I started cleaning the D3!!
The sensor seems to attract more dust than that of the D2x.
As the sensor is bigger (full frame) and fills the whole mirror box, it's not possible to wipe over its sides, where it wouldn't matter if any specks remain.
In the beggining, not taking enough care, I had several big smears across the whole sensor which I only got rid after strong wet cleaning.
So beware, cleaning the D3's sensor is possible but you have to be careful.
I actually also always first use the Visible Dust sensor loupe to check the sensor and only clean it if necessary.
But nevertheless, I love the D3 and also use the new outstanding 14-24mm (and 24-70mm) a lot with great success.
Good luck with cleaning!