Surface-enhanced Raman scattering is capable of providing rich vibrational information at the level of single molecules and single nanoparticles, but the practical applications of this enormous enhancement effect are still a challenge. Here we report a new class of dye-embedded core-shell nanoparticles that are highly efficient for surface Raman enhancement and could be used as spectroscopic tags for multiplexed detection and spectroscopy. The core-shell particles contain a metallic core for optical enhancement, a reporter molecule for spectroscopic signature, and an encapsulating silica shell for protection and conjugation. A surprising finding is that organic molecules with an isothiocyanate (-N=C=S) group or multiple sulfur atoms are compatible with silica encapsulation. In comparison with fluorescent dyes and quantum dots, enhanced Raman probes contain a built-in mechanism for signal amplification and provide rich spectroscopic information under ambient experimental conditions.