Actually, the R34 GT-R V-Spec N1 isn't the fastest, at least when tuned. The V-SpecII Nür overtakes it thanks to a higher power output.
A pretty thorough detailing follows.
R32
GT-R: The base model, the lightest, but also the one with the worst tyres and suspension. The lightest of all GT-R Skylines.
GT-R N1: A version aimed for track use, equipped with different turbos and other minor equipment changes.
GT-R V-Spec: A refined model with a bit more weight, larger wheels and better suspension, and higher power output.
GT-R V-SpecII: An even more refined model with slightly wider tyres than the V-Spec. The best one out of these.
R33
GT-R: Again the base model.
GT-R N1: A similarly track equipped one as the R33 N1.
GT-R V-Spec: A refined model featuring better suspension and a more sophisticated four wheel drive system. The best one out of these.
GT-R V-Spec LM Limited: Just a V-Spec built to celebrate the Le Mans success of the GT-R.
R34
GT-R: Again the base model. The drivetrain of the R33 V-Spec fitted as stock.
GT-R V-Spec: A similarly refined model as the R33 V-Spec.
GT-R V-SpecII: An even more sophisticated fast car, with technical improvements here and there.
GT-R V-Spec N1: A similarly track equipped car as the R32 & R33 N1, based on the V-SpecII.
GT-R V-SpecII Nür: A special version of the V-SpecII, featuring better turbos and some interior changes. The best one out of these.
GT-R M-Spec: Something of a luxury GT-R, featuring a slightly softer suspension than the V-Spec and a leather interior. Technícally similar to the V-Spec.
GT-R M-Spec Nür: Like the V-SpecII Nür but built out of a M-Spec. The heaviest of all GT-R Skylines.
The Nismo models
GT-R S-Tune: The ultimate R32, it comes with a high revving engine and a very responsive handling. Based on the R32 GT-R V-SpecII.
400R: The ultimate R33, with loads of power in the lower revs but a bit asthmatic top end. Based on the R33 GT-R V-Spec.
GT-R R-Tune: The ultimate R34, pretty similar in style to the S-Tune but handles like the R34. Based on the R34 GT-R V-SpecII.
My personal favourite is the S-Tune, combining the handling of the old school R32 to the technology of today. It's pretty hard to drive really fast though, the best models for beginners are the R34's thanks to their more docile cornering characteristics.
All the things that can be tested in GT4 have been tested, naturally the things like the leather interior of the M-Spec are taken from the web. By the best I don't mean just the stock models but also the tuning capabilities. I've always felt the V-Specs to handle a bit better when compared to the base models, that's personal preference of course.