Depends. Biodiesel, e.g. from soybeans, produces 3.2 units of fuel for every unit of (fossil) fuel input, according to the USDA. A German study came up with a number of 2.5 to 1. That's still a pretty good deal.
Ethanol from corn barely breaks even. Don't tar all biofuel with the ethanol-from-corn brush. Ethanol from corn is only viable because it's subsidized by government.
All bio-diesel shortens engine life, increases maintenance costs, and reduces the reliability of the engine.
It also cannot be used below 40 degrees F, because it thickens in the fuel system, thus starving the engine.