The biodiesel.org site, which is run by the National Biodiesel Board (a biodiesel industry trade group), references [1] a 1998 study that shows biodiesel to have a 78 percent reduction in net CO2 emissions. So not carbon neutral, but significantly less net emissions. I'd be interested in seeing the results of a more up-to-date study.
However, that's the net reduction for B100, or 100% biodiesel. The more common and engine-friendly B20 blend at 20% biodiesel / 80% petroleum diesel would be a 15.6% net reduction in CO2.