Run, don’t walk, to back40’s house at CrumbTrail to read this post and the article to which he links on the dubious reasons for claiming that biofuels are renewable.
It has bothered me for a long time that no one has really quantified the entire supply chain in modern biofuels, including all of the attendant energy flows in producing fertilizer, transportation (which for things like ethanol is substantial because ethanol is the fragile flower of the fuel world), and so on. This article and post at least point us in that direction, although much, much more analysis is required.