In terms of biofuels, there is simply not enough feedstock available. Even if there were enough feedstock to replace all the oil products we use today, there are many other potential uses which will compete for the output of scarce land and water, such as a replacement for coal in electrical generation, and fodder for livestock. Biodiesel producers may find that the best quality oil is bought up by refineries to make green diesel instead.
No one knows how the limited feedstocks we have available that will be used, or what process will be most efficient in converting them into their final form. Higher commodity prices do not always lead to more supply. Sometimes higher prices lead to lower demand, and the next boom could easily become the next bust.
The only sure winners from limited and increasingly valuable biomass will be the people who produce it: farmers, foresters, and (perhaps) trash haulers and recyclers. What do farmers do when they have spare cash? They buy farm equipment, quite often from Deere & Co. Few stock have ridden the biofuel boom as well as Deere, with the stock rising 400% in the last four years in a nearly uninterrupted uptrend, without the thrills and spills that have turned so many investors off of corn ethanol.
The beauty of Deere as a biofuel investment is that there is no need to know what the biomass will be used for, or what form it will come in. Deere is likely to be a major supplier to the industry which grows bio-fuel. From algae, to forestry to Jatropha, if Deere does not yet sell equipment to plant, tend, and harvest it, it seems a good bet that they will design one.
This technology agnosticism, combined with their wide dealer network in agricultural areas, makes the company seem to me the safest way to bet on biofuels as a trend.