The great thing about CO2 emissions for plant-derived biofuels is that they won't modify the chemical composition of the atmosphere. Think about it for a moment: what you're doing is extracting carbon from the atmosphere, turning it into complex hydrocarbons using energy from the sun, and then burning it to release that energy. Any CO2 released was *already in the atmosphere* to begin with, so biofuels net zero greenhouse emissions (to first order at least, maybe there's some weird combustion products or whatever). Hard to get much lower than that.
Well, yes and no. Biofuel will only be carbon neutral if all the production, transportation and fertilization was done with biofuels as well. A great goal, but I don't think it's been realized anywhere yet.
And of course, that still leaves the whole fuel vs. food issue open. Now if we could manage to come up a biofuel production process that includes the net fixation of atmospheric CO2 (net reduced or zero carbon footprint), with close to zero ecological impact that is not using precious agricultural land then I'd be all over it. But at the moment it's a bit of a pipe dream.