This guy has a short post about whether or not motorcycles are "green." I'm not an expert, but I really think we have to take more into consideration than just emissions when we're trying to judge the environmental friendliness of a given vehicle.
For example, how many resources does a given vehicle consume when being produced? How many resources does it consume to keep it mobile? What happens when the vehicle is scrapped? How long will it last until it needs to be scrapped?
Another thing to consider is the impact of motorcycles on how friendly your environment can be. I don't see too many cagers with huge grins on their faces when they're sitting, alone in their cars and trucks, in commuter traffic. I don't know if it's measurable or not, but that mess has got to be bad for our national psyche. On the other hand, I haven't met too many grouchy bikers on my ride to work (though there are always a couple oddballs).