I've spent the last 5+ years cautioning people about the hazards of biodesel. If you listen to the gov' experts and tree huggers, you would think that this magical fuel was going to save the planet by itself.
From a Cummins perspective, we remind our customers that ANY fuel additive that causes a failure in the engine is not covered by the Manufacturers warranty. Some people have said that using biodiesel voids the warranty, but that is simply not true. Cummins approves biodiesel use I blends up to 20% for certain engines in our lineup. 5% is considered a normal blend that you can find at a pump. Cummins prohibits the use of Biodiesel in stand by generators, and we caution recreational and commercial marine customers from using it at all.
The reason for these two exclusions is based on biodiesel's ability to hold water. Water in fuel tanks on boats or with generators don't turn over fuel much, and condensation forms in the tanks and is kept in solution through the biodiesel molecule. Water is an engine's fuel injector's worst enemy, so any avoidance of water in fuel is imperative.
As far as using in trucks and cars......if you put biodiesel in an older storage tank or onboard fuel tank, the caustic nature of biodiesel will clean out the tank and fuel lines. You'd be replacing fuel filters more often until all the sludge is removed from the fuel system. biodeisel is also hard on painted surfaces, so beware of spilling during refueling.
If you feel that you need to save he planet, and need to use biodiesel, make sure you buy from a really good supplier, and one that rotates his stock on a frequent basis. If you live above the Mason-Dixon line, I would avoid biodiesel during winter months, as it will gum up your fuel system when the temp begins to drop. The major biodiesel retailer in Boston tells people not to use hi blends between Haloween and St. Patrick's day.