[I]According to the September 2009 issue of FastBikes Magazine (Fast Bikes), both bikes have been given equal ratings.
The Yamaha R6 is a high performance bike on the track, but on the road they claim it to be a bit "allergic" to power gains. They also say it has a bit stiffer suspension (because its more race spec) and may be uncomfortable to ride for a longer period.
The Honda CBR600 according to them is "better than the R6 on the road but it just lacks balls and a decent setup to show its promise". Its more comfortable to ride than the R6 but it is just more "fashion than function"
I'd recommend the Yamaha R6. Why? Because we people are used to riding stiff suspensioned bikes. The CG125 for example isnt a heavenly thing to ride - but we all enjoy riding it. Plus the thing they mentioned about it being a pain to ride on the road, lots of people commute long distances to work on sport bikes (in the UK) so maybe it may not be that fun to ride it on the roads there than it is on the track.
Where are you from? If you're from Karachi, you have great roads at Devil's Point or sea-view to thrash the bike. If you are in Lahore, you can cruise down the Canal Road in the evenings or late at night when there's little traffic. If you're in Islamabad, then, lol, you can thrash it anywhere you want, the Isb-Pindi highway, Margallah Road, 7th Avenue, 9th Avenue - you name it, its upto you. And I am sure you wont be riding the bike in peak rush hours...
If I was in your shoes, I'd go for the R6, because a bike like this is meant to be thrashed (not abused though), and if you are that sort of person who loves to take a bike to its limits, this is the bike for you!
Check out these ratings. Top rating is 5 per category. The categories (from left to right) are: Track, Fast Road, Hooligan (i.e. stunting capabilities), New Rider (learning curve of the bike for a new rider) and Desirability:
And these are the CBR600's ratings: