Microbial production of biofuels often places many different burdens upon the cell, and understanding these burdens is critical to ensure the generation of a robust, industrially useful strain. The past two decades have seen an explosion in the amount of cell-wide data being produced, including microarray, proteomics, and metabolite analysis. Industrially applicable strains such as Escherichia coli, Bacillus subtillis, and Clostridium and Zymomonas species have been especially well studied. While few of these studies have actively focused on biofuels production, many experiments have been conducted on related issues that are sure to impact biofuels production, such as the metabolic burden of exogenous genes, environmental stress response and adaptation, stationary phase response, and more. In order to capitalize on research that has already been completed, a review of literature has been conducted. We present many common trends between these different studies, and highlight considerations that should serve as a starting point for any microbial biofuels production platform.