As a consequence of current energy and climate policies, several regional and federal measures are being implemented in Belgium to encourage the utilization of biofuels for automotive applications. The use of biomass for power and/or heat production also gets growing support through CHP and/or CO2 certificates and most probably through new upcoming European directives. As a result, many investors, policy makers and energy companies are investigating these so-called biomass routes and there is definitely a need to gain more insight in this complex matter. This paper presents an analysis and comparison of the most promising options for utilizing the limited biomass resources in Belgium. To allow for a systematic comparison, a new method called System Perturbation Analysis (SPA) was developed. SPA differs from a classical Life Cycle Analysis (LCA) mainly because it looks to geographical system balances of resources and the resulting effects, rather than comparing well-to-wheel trajectories. Therefore SPA is able to identify the best usage of limited resources such as hectares, wood waste or imports, in terms of fossil energy savings or GHG emissions within a given system (in casu: Belgium). Comparative results of such a SPA assessment are presented and discussed in this paper, including the use of wood for transport, heat and power applications. All the considered biofuel scenarios have positive energy and CO2eq balances. The use of wood appears as a good choice in terms of efficiency, CO2 abatement and surface requirements.