The Examiner has a good comparison of the pros vs cons of using biodiesel.

According to the Examiner, the pros are:

" It’s eco-friendly—about an 80 percent reduction in greenhouse gases
• Significant reduction in sulfur
• 90 percent reduction in cancer agents
• When blended with standard transportation diesel, biodiesel helps to extend
the energy capacity of the diesel
• It can also be used as a home heating oil
• It is less combustible than petroleum, making it safer to store and transport
• If biodiesel spills, it is biodegradable and breaks down roughly four times faster than petroleum diesel
• Runs in any conventional, unmodified diesel engine"

while the cons are

"

• It would take a lot of land to create enough biodiesel to put an end to the oil crisis conflict. Statistically to produce just five percent of the total diesel consumption of United States, approximately sixty percent of the crops would have to be diverted towards the production of diesel
• The use of biodiesel results in increased levels of harmful nitrogen oxide (NOx)
emissions when used in diesel engines, although not usually in residential heating equipment. Biodiesel also releases the same amount of hydrocarbon
(or soluble carbon) emissions when burned as regular diesel
• Pure biodiesel has a high "clouding" point, meaning that liquid biodiesel begins to thicken into a solid at low temperatures. Because of its higher clouding point, biodiesel is more difficult to store and transport in cold climates, which adds to its cost
• Regarding its use in vehicles, purchasing used restaurant cooking oil locally and either making your own biodiesel at home or via an aftermarket system that is installed in your vehicle may not be such a good idea. In general it does not perform as well as petroleum diesel in cold weather, and biodiesel made from used cooking oil is even more significantly affected by cold weather than that made from soybeans. In simple terms, cold temperatures cause biodiesel to turn to a gel-like substance, which in turn can cause a whole host of engine problems like fuel filter clogging, severe engine lubricant degradation and carbon deposits, just to name a few…"

We think the pros far outweigh the cons. There are chemicals to lower the cloud point so that cold weather usage can occur. We talked more about it here . And, there are studies underway to show the NOx level can be controlled. What do you think?