As John mentions there's quite a bit to look at for the various impacts for growing additional crops for biofuels, but basically it boils down to developing effective new stnadards for this emerging industry. Diesel in general has different emissions than gasoline, with its main nasty emission being mono-nitrogen oxides which contribute to acid rain. Diesel emissions are commonly about twice that of gasoline, but most people fail to realize that diesel delivers three times the energy of an equivalent volume of gasoline meaning it actually nets less. Again, government at work.

Another misunderstanding about biodiesel among most is its confusion with vegetable oil, either in straight (SVO) or waste (WVO) source-stocks. Biodiesel is a fuel processed from vegetable oil and is 100% compatible with all diesel engines, whereas vegetable oil works best in older vehicles (generally pre-1987) using mechanical indirect injection. It can be run in newer engines but requires a two-tank system where you start and shut down the engine on diesel, running the rest of the time on vegetable oil. An interesting thing happens when you run a diesel on vegetable oil, the distinctive "clatter" goes away. Then again, Rudolph Diesel designed it to run on vegetable oil to begin with.

Ironically the biggest hindrance to the alternative fuel industry is that there are simply so many alternatives. The general public finds it far easier to pony up $$$ at the pump rather than learn what's out there and sort through all the hype and hyperbole.