That said, I don't know where the OP got the idea diesel was cleaner than gasoline.
Diesel is still a bit more efficient overall, start to finish. It takes less energy to produce, and you do still get more mileage from a diesel even though TGDIs are closing the gap. They thus produce less CO2/mile, though they do produce more NOx. However, they also release fewer unburned hydrocarbons, because the basic function of a diesel is to run lean all the time (hence the NOx.) They also tend to produce torque at low RPMs, where there's less loss due to friction. All this still arguably adds up to diesels being less polluting than gasoline vehicles, now that we know that the gassers produce just as much soot as the diesels.
The cleanest fuels of which I'm aware overall are butanol and methane. Butanol can be made by bacteria from any organic material, and is a 1:1 replacement for gasoline. The other stuff that comes out of the same process (ethanol and acetone) can be used to adjust octane. Butanol produces less emissions than gasoline when used as a motor fuel. Acetone is already commonly used as an octane booster and to reduce emissions during testing, although it takes quite a bit to make a significant difference. Methane is a common byproduct of decomposition in nature as is, and when you burn a gas like methane or propane in a combustion engine you substantially reduce both emissions and wear not just to the engine parts themselves (you'll never wash the walls of the combustion cylinder with methane or propane) but also to the crankcase lubricant. Since the fuel burns cleaner, the blow-by is cleaner, and the oil lasts longer. With simple and relatively minor hardware changes (mostly the addition of solenoid valves and spray nozzles, plus probably an additional computer module) engines can be made to run on both fuels, including startup.
Where does the methane come from? AIWPS. Ah, we can dream of a world gone sane.