Residues and waste are by-products from biological material harvested mainly for non-energy purposes. The most important by-products are wood residues, agricultural residues and municipal/industrial waste:

Carbon payback time is the time it takes before this carbon is "paid back" to the forest, by having the forest re-absorb an equivalent amount of carbon from the atmosphere.

The spatial boundaries define "geographical" borders for carbon emission/absorption calculations. The two most common spatial boundaries for CO2 absorption and emission in forests are 1.) along the edges of a particular forest stand and 2.) along the edges of a whole forest landscape, which include many forest stands of increasing age (the forest stands are harvested and replanted, one after the other, over as many years as there are stands.) A third option is the so-called increasing stand level carbon accounting method:

– In stand level carbon accounting, the researcher may count a large emission event when the stand is harvested, followed by smaller, annual absorption amounts during the accumulation phase that continues until the stand has reached a mature age and is harvested again.

– Likewise, in increasing stand level accounting, the researcher counts a large emission event when the stand is harvested, followed by absorption of smaller quantities of carbon each year during the accumulation period. However, one year after the first harvest, a new stand is harvested. The researcher do not count the carbon that was absorbed in this second stand after the first, neighbouring stand was harvested, only the large emission at the harvest event of the second stand. The next year the same procedure repeats for the third stand; the carbon that was absorbed by this stand after the harvest of the first and second stand is not counted, while a large emission amount is counted when the third stand is harvested. In other words, in increasing stand level accounting the whole carbon account is composed of a number of individual stand-level accounts, each with its own, individual starting point.

So, the researcher has to decide whether to focus on the individual stand, an increasing number of stands, or the whole forest landscape.

The assessment of such "additional fellings" from "new" bioenergy plantations after the first rotation is complete, depends on the chosen carbon accounting method. If the "early" carbon accounting continues, there will be a build-up of a carbon credit also after the first rotation, i.e. from the moment in time when the trees have been replanted. If the researcher at that time change to "late" carbon accounting, no carbon credit will be calculated, and at the end of the second rotation (at harvest) a large carbon debt will be created instead, causing payback and parity times to increase dramatically.

The problem can be dealt with both from the perspective of increasing the amount of carbon that is stored below ground, and from the perspective of decreasing fossil fuel input to the above-ground operation. If enough carbon is stored below ground, it can compensate for the total lifecycle emissions of a particular biofuel. Likewise, if the above-ground emissions decreases, less below-ground carbon storage is needed for the biofuel to become carbon neutral or negative.

The reason for the low power density for some of the biofuels is a combination of low yields and only partial utilization of the plant (for instance, ethanol is typically made from sugarcane's sugar content or corn's starch content, while biodiesel is often made from the oil content in rapeseed or soybean).