Several interesting effects discovered recently, such as “dynamic blocking” and “jamming” of emulsion flows in microchannels require in depth theoretical, computational, and experimental studies. The present study is dedicated to development of efficient computational methods and tools to understand the behavior of complex two-phase Stokesian flows. Application of the conventional boundary element method is frequently limited by the computational and memory complexity. The fast multipole methods provide O(N) type algorithms, which can further be accelerated by utilization of graphics processors. We developed efficient codes, which enable direct simulation of systems of tens of thousands of deformable droplets in three dimensions or several droplets with very high discretization of the interface. Such codes can be used for detailed visualization and studies of the structure of droplet flows in channels. Example computations include droplet dynamics in shear flows and in microchannels. We discuss results of simulations and details of the algorithm. We also consider that the present work is a step towards more realistic modeling of the microchannel dispersed flows as further development of the model is required to account for properties of thin films between the droplets, processes of coalescence, etc.