Silver nanoparticles tagged with dyes and encapsulated within a silica layer, offer a convenient potential substrate for performing multiplexed surface-enhanced Raman scattering (SERS) analysis. In contrast to our earlier work with gold particles, aggregation of silver particles is found to be mostly independent of dye addition, allowing for a reproducible preparation in which aggregation is actively induced by the addition of NaCl. Separating the aggregation step eliminates competitive binding between the dyes and silica-coating reagents, enabling the efficient use of a wide variety of weakly binding dyes to conveniently generate robust, high-intensity SERS substrates at a variety of excitation frequencies.