I've yet to see an organism that secretes hydrocarbons insoluble in water and surviving. A living organism can produce ethanol until its mass ratio in the water solution reaches ~16%, then it dies. You can separate ethanol from water only by distillation, and since there's 84% or more water in the solutin, you will have to spend lots of energy, and your ethanol fuel will have a low EROEI (energy recovered on energy invested). With buthanol, which is a better fuel than ethanol and less soluble in water too, the mass ratio goes up to 4% until it kills the producers. Unfortunately, buthanol is partially miscible with water, and at such low concentrations you will have to use distillation, and since it's boiling point is higher than that of water, you will have to boil off all the water until you get reasonably pure buthanol.
A solution to this problem would be if an organism would secrete fatty acids. Fatty acids are insoluble in water and are high in energy content, and they would simply float on the surface where you could gather them without spending much energy. However, the fatty acids (and for that matter anything insoluble in water or other polar solvents) are soluble in the cell membranes (which are made of lipids (fat!)) and there they could destroy the membrane, making it overly big and water surface tension forcing it to separate into mycelles, causing loss of cholesterol and fosfolipids from the membrane, therefore jepardising membrane functionality.
I highly doubt that genetic engineering will solve this chemical problem any time soon. I think solar, wind and nuclear are the way to go, but unfortunately, they can only supplement fossil fuels, not replace them.
