More tolerable costs, instant recharges, and increasing energy density demands make fuel cells ideal for supplanting batteries in portable electronic devices. Analytical and semi-analytical models are derived in this thesis to elucidate the transport of ions, heat and mass within two different ambient air-breathing fuel cell architectures. The first architecture is the conventional planar arrangement and the other is a microstructured non-planar architecture. An analytical model of the membrane electrode assembly accurately predicts fuel cell performance through detailed accounting of catalyst layer specifications and electrochemical parameters. A largescale parametric study resolves the trends associated with a variety of design specifications and operating conditions. The study identifies the substantial effect of heat transfer on membrane dry-out and demonstrates a need to insulate humidity within the fuel cell to enhance performance. An analysis of the non-planar microstructured fuel cell reveals its increased power density and efficiency.