We employ a semi-ab initio theoretical method to investigate mode confinement, interface mass-smudging, and sample length effects on phonon transport in thin nanocomposite superlattices. We present a detailed comparative study of numerical results showing the reduction in thermal conductivity due to each of these three effects for Si/Ge nanocomposite structures with planar superlattice (SL), embedded nanowire superlattice (NWSL), and embedded nanodot superlattice (NDSL) geometries. Importantly, it is found that any of these three types of thin period systems, with small amounts of interface mass smudging, can exhibit a room-temperature conductivity significantly lower than the SiGe alloy conductivity, providing strong evidence that they could be used as efficient thermoelectric materials. It is also found that the room-temperature conductivity of each of the nanocomposite superlattices shows a weaker sample size dependence than do the component bulk conductivities.