Heat transfer and fluid flow through different microchannel geometries in the transitional regime (rarefied flow) are analyzed by means of direct simulation Monte Carlo (DSMC) simulations. Four types of three-dimensional microchannels, intended to be used as expansion slots in microresistojet concepts, are investigated using nitrogen as working fluid. The main purpose is to understand the impact of the channel geometry on the exit velocity and the transmission coefficient, parameters which are well known to affect directly the thruster performance. Although this analysis can be applied in principle to several possible microfluidics scenarios, particular focus is given to its application in the field of space propulsion for micro-, nano-, and picosatellites, for which the requirements ask for low thrust levels from some micronewtons to a few millinewtons and moderate specific impulse, as well as a low power consumption in the order of a few watts. Analysis shows that the thrust produced by one single microchannel can be increased by about 480% with a careful selection of the channel geometry, decreasing at the same time the specific impulse by just 5%, with a power consumption decrease of more than 66.7%.