I've been looking for an excuse to mention the now-week-and-a-half-old release of a report that NRDC supported on the importance and complexity of creating an index of the environmental characteristics of different gallons of different biofuels. I've talked to a number of reporters about it and gotten a lot of positive feedback, but the only reference to it I've found so far appears to come at it from the angle that all biofuels are inherently bad so an index is a waste of time.
Of course most technologies are not inherently good or bad; it all depends on how you use them. And an index or certification system is a necessary but not sufficient tool in using biofuels right.
In any case, I highly recommend the report by Turner, Plevin, O'Hare, and Farrell from UC Berkeley. It's called Creating Markets for Green Biofuels. It's not a how-to manual, but it does a great job of explaining why the production practices can make such a big difference in weather a gallon of biofuels contributes environmental benefits or imposes environmental costs and the many challenges to accurately, affordably, and usefully reporting the environmental performance of biofuels. You can find the report here and NRDC's press release on the report here.