Depends on the application. The belts of modern components are good up to 125 hp. Put them on street cruisers for the most part.
Chains are better for applications with dirty conditions, manuvering, and use above 125 hp.
Shaft drives are good for any size motor and torque. Good for touring and straight line driving. Easier to keep a bike clean. Modern shaft drives are even good in the curves with power applied.
I have owned all three, and basically use these guidelines for picking.
I currently own a Triumph Rocket III Classic Tourer(140 cubic inches, 140hp and 147lbs. torque) with a shaft drive. I also owned a Dual-Sport 125 hp bike(chain drive), and a 90 hp v-twin street cruiser(belt drive). No problems with any of these drives, as long as I kept them in their performance parameters.
If I had to pick one, it would be a chain drive. But not necessarily the convenient choice in all applications. But a chain drive will get it done.