See: http://rael.berkeley.edu/EBAMM/ERG-NPR-letter-1-30-06.pdf
Farrell agrees with Pimentel that ethanol takes a lot of input energy -- although he does not specify how much in this letter. He says that Pimentel was wrong and that the Berkeley study did take into account the energy used by farm machinery.
His main point is that much of the input energy for ethanol production comes from fuels other than oil, so it produces a net increase in transportation fuel. Maybe so, but I doubt it is economically viable, I doubt it does anything to reduce CO2 emissions, and I expect that if the subsidies were withdrawn no one would buy the stuff.
- Jed
