We report on a study of the overall surface-enhanced Raman scattering (SERS) response from several thiol-terminated molecules located at interstitial sites between Ag nanoparticles. Multiplexing of the SERS signal was demonstrated along with its dependence of the molecular length, regiochemistry, and the number of thiol groups. The data collected establish pathways for the rational design of the SERS reporters and multiplexed sensory applications.