http://www.uidaho.edu/bioenergy/NewsReleases/Biodiesel%20Energy%20Balance_v2a.pdfHowever, I have some problems with BioDiesels fuel.
Currently, to produce the fertilizers at the scale we use (and an even larger scale if we start consuming a lot of biodiesel) requires a lot of "natural gas", a fossil fuel. Making the pesticides at the scale we are now (and again if we start using a lot of biodiesel the production of pesticides will have to increase) uses large quantities of oil.
That is the nature of the best. You are just trading where the fossil fuel is used. Now, that does not mean they use the same amount, but it is still a problem.
In order for biodiesel to really be successful (financially and environmentally) those two serious issues will have to be addressed. But again, this is something chemistry will address!
I also think that another thing that will greatly help biodiesel and make it more useful on a large scale is either genetically modifying the plants or selective cross breeding (as humans have done through our history to make the wonder fruits and vegetables we love now) to improve the amount of biodiesel that can be made per unit of plant, lowering cost and improving efficiency.
But in my opinion, the fertilizer and pesticide problem is the current biggest problem that needs to be addressed.