If you worry about carbon dioxide emissions that come from any activity it is easy to ask questions that are very difficult to answer. A case in point is corn methanol. Growing the crop takes a lot of water and that requires energy as does farming and the use of fertilizer. Some suggest you must take a larger view and look at existing crops that are displaced in order to grow more corn. Many studies show it is not a very efficient way to cut carbon dioxide emissions and some show net carbon emissions may be greater than gasoline.
Other biofuels, like biodiesel derived from waste oils may be green as they simply make use of a product that would normally be thrown away where it would decompose and emit carbon anyway, but these schemes don't scale. On the horizon are second generation biofuels like algae. They have the potential to be much better than corn ethanol, but they are some years from production and there may be scaling issues.
But some argue that the full carbon cost of oil from the mideast has not been calculated. Two professors from Nebraska argue that a proper accounting of gasoline must include the portion of military actions that are deemed necessary to protect US energy interests in the area. Wars use a huge amount of fuel. These are probably calculations that are impossible to get any accuracy on, but one can set limits.
My own preference would be to eliminate subsidies that have very poor carbon efficiencies - ethanol would rank high on my list - and to focus on efficiency and conservation in the short term. But huge lobbies and the lack of sex appeal for conservation and efficiency mean that such a course is extremely unlikely.