First, the ZX 6R isn't THE BEST. Don't get me wrong, I love the ninjas. A hell of alot more than any ot the other inline 4's from Japan. But to be honest, it isn't the best one. Before 08, it was probably the CBR RR, since it was reliable, powerful and handled like a dream. In 08 the R6 recieved great praise for its track abilities and won the 600cc section of the Master Bike competition, over the CBR, the Ninja, and the Triumph Daytona 675. I mention the Triumph because it recieved Motorcyclist magazine's Motorcycle of the Year award in 2006, and is famous world wide for handling like a dream. In the 08 master bike competition, it actually got second to the R6 and recieved the best ratings from the riders, (it just couldn't put out quite the same lap times as the R6).
So when you buy a Ninja, you aren't buying the cream of the crop. Though you'll notice I didn't give any praise to the Gixxer, because it actually isn't better than the Ninja (in my opinion). But you are buying a bike with styling like no other, and with plenty of power to keep up with the rest. All of these bikes have more power and better handling capabilities than can ever be used in the streets, and can only be fully appreciated by professionals on a track, so you don't NEED the BEST one.
That said, the question becomes this. Is it the styling, or the power you want more? The Ninja from 05 to 08 was plenty powerful, and I believe the 07 and 08 versions were more powerful than the 636. But the 636 will be cheaper, and had a bigger displacement, so will have plenty of potential to be as strong or stronger, if worked on properly.
As the guy who first responded said, the new for 09 Ninja is certainly better than the others as far as track capabilities go. There's no question. But it's also going to cost you up side of 10000 dollars. I don't think it's worth it considering it's pig ugly exhaust, but it may end up being the race bike of the year in 09 considering all the upgrades.
It's your call. I personally fell for the 08 at first sight and wouldn't want anything more except a Ducati 848.
