According to the Cornell press release (I haven't been able to read the actual article yet), Pimentel and Patzek find conversion of various plant products to ethanol or biodiesel to require MORE fossil fuel than the resulting bio-fuels displace, at least under North American conditions.
From their numbers, for ethanol production:
Green Car Congress and WorldChanging have lively blog commentary - there may at least be some bias from Patzek's sources of funding - but nobody seems to have numbers that completely disprove what they're talking about. Pimentel is quoted in the Cornell press release as pushing for investment in solar and wind, and producing electricity from burning biomass, which seems a pretty sensible plan.