There's minor (very minor) differences between team cars in the modern GT500 cars ('07 onward). But, the differences in performance are probably smaller than the differences between your fastest and second fastest lap times.
If you're after the fastest one, go for a 08 GT-R, one of the factory entered ones. It's the fastest of the newest ones.
The GT300 cars, on the other hand...there's a range to chose from, and the best depends on whether you're going to tune it. If you're not, go for the latest model. Doesn't really matter, just pick what one looks best.
If you ARE going to tune it, keep an eye out for the WedsSport Celica in the Used car dealership. It actually uses a 2002 Toyota Supra GT500 engine/drivetrain that's been detuned a bit to fit into GT300 (read the description for this car, it'll make more sense). Whack a turbocharger on it and it'll make a nice easy 400hp, but with a shorter wheelbase and fairly aggressive aero it can (at times) out-perform GT500 cars, especilly around and through the corners and under brakes. AND all up it costs $200,000 for the car and $60,000 for tyres and a turbo.
Bargain, if you ask me.
AND it looks good. Almost like a permium.