Owning both, I'd have to say that the bikes will win almost every time...in the straights. All of mine are relatively stock, 450hp for the Viper, 110hp for the GSX-R600, and 160hp for the GSX-R1000. It's the horsepower to weight ratio that give the advantage to the bikes. Look at the liter bike compared to a 2008 Viper. 600hp at 3440 lbs for the Viper vs. 160hp (RW) at 379 lbs on the liter bike. Most newer bikes are governed, voluntarily by the manufacturers, at 186 mph...but they get there quick.
Car and Driver, Road and Track, Motorcyclist Magazine do a comparison almost every year with various cars and bikes. On the drag strip the bikes always win. On the track, the last one I remember reading was an 06 Viper vs a YZF1000 and the Viper won. A recent test had a Veyron up against a Busa. Here's the numbers, both stock:
Power:
182bhp (measured at rear wheel) – Suzuki Hayabusa
1,001bhp (measured at crank) – Bugatti Veyron
Horsepower to Kilogram:
.827 – Suzuki Hayabusa
.53 – Bugatti Veyron
0-60mph:
2.74 seconds – Suzuki Hayabusa
2.46 seconds – Bugatti Veyron
1/4 mile:
9.985 seconds – Suzuki Hayabusa
10.2 seconds – Bugatti Veyron
0-186mph:
18 seconds (184mph restricted top speed) – Suzuki Hayabusa
19.8 seconds – Bugatti Veyron)
The Busa is not a good 0-60 bike, it's made for top speed, once its unleashed (no governer). Most of the liter bikes now pull 0-60 at around 2.5.
The biggest disadvantage for the bikes is usually the rider. It takes a lot more skill to make a bike go fast than it does to make a car go fast. Of course, it takes a good amount of skill to put down torque, but on the road, most of us don't have to worry about keeping the front wheels down in a car.