Obviously, the Nikon is clearly the better lens, both optically and mechanically, and it also comes with a five year USA warranty and will have high resale value compared to a Sigma. VR is nice for smoothing out really slow-speed pans, like those done at 1/3 to 1/15 second, when you want to really convey a fluid motion blur type of feeling. VR really helps quell camera movement, and it allows you to shoot in low light situations without a tripod, and keep the camera steady, so it's valuable in that area. I dunno...I bought the VR-1 the week it came out, and payed $1699, back in April of 2003,and the lens has held up very well and has held a lot of its value; a Sigma will not hold nearly the same value percentage.
I think the 70-200 f/2.8 lens category is one where the camera-maker lenses are clearly the better lenses. If you go with the Nikkor, you'll also have the advantage of the newer Nikon teleconverters, like the excellent TC1.4e-II and the TC17e, as well as the brand new TC-20E-III Aspherical telephoto converter, which is pretty much unlike any other company's teleconverter, and which offers a whole new level of teleconverter performance, due to it being the only TC unit with aspherical optics and which is optimized for the "new Nikkors". The new TC20e-III (3rd generation) does amazingly well on the new 70-200VRII lens,as well as the 200mm f/2 and 300 f/2.8VR lenses. The TC14e-II is a pretty good choice as a one-stop light loss converter that will give you a 280mm f/4 equivalent without much loss of quality as long as the lens is stopped down one stop from f/2.8 or more.
Overall, given how important a 70 to 200mm focal length range is--it is basically six or seven well-recongnized individual telephoto focal lengths all in one lens, I think the added focusing speed of the Nikon lens, the optics of the Nikon at wide-open as well as across the entire focal length range, and the suitability of the NIkon lens to three converters, makes the Nikon worth the extra money. This is a lens you can have and use for a decade,or longer. And, when you sell it after a decade, you will get back about the same number of dollars you sunk in to buy it--try that with a 10 year old car, or a 10 year old Sigma or Tamron.