Molecular dynamics simulations are used to investigate the diffusive flow of binary molecular mixtures through single-walled carbon nanotubes. Both H-terminated and C-terminated open nanotube ends are considered in the study. The specific mixtures examined are methane/ethane, methane/n-butane, and methane/isobutane. The simulations predict which binary mixtures separate as a result of this diffusive flow and which remain mixed and how these results depend on the nanotube properties such as diameter and helical symmetry. The simulations also indicate how the structure and size of the molecules in the mixtures influence the results. For example, n-butane and isobutane are predicted to have significantly different separation behaviors when they are mixed with methane molecules. In addition, the degree of separation predicted depends on whether the nanotubes are in bundles.