Like any other technology, bioenergy has a spectrum of advantages and disadvantages associated with it. Biofuels, for instance, are expected to reduce the dependence on foreign oil considerably, but the energy balance and carbon emission savings achieved by biofuels is still under question. However, amidst all this debate, global bioenergy development continues to take place and is being studied and investigated by scientists, engineers and government agencies worldwide. Simulation, modeling and analysis of bioenergy systems is an inherent and critical part of this process. The first part of this thesis deals with the detection and subcategorization of hard-coding errors (a prominent type of spreadsheet error) in bioenergy-relevant spreadsheets. The second part of this thesis deals with the life cycle analysis of six kinds of cropping systems for bioenergy production, including conventional and alternate; and their assessment from various standpoints of energy, net productivity, and adverse environmental impacts.