Surface-enhanced Raman scattering (SERS) has attracted considerable interest as a sensitive vibration-specific probe for bioanalytical and imaging applications. Among the various bioprobes available, Ag-embedded SERS tags have been rigorously developed for an extensive range of biodetection applications. In this review, we look at the additional functionality that SERS tags can offer via its magnetic properties, fluorescence, and an extension of the optical region into the near-infrared (NIR) spectrum. Such functionality can be achieved by using Ag nanoparticles (NPs) or Au/Ag hollow-shells (HS) as a SERS signaling unit, with SiO2 nanospheres providing a back-bone unit. This back-bone can include a magnetic core (M-SERS dots), but also provides an outer shell that protects the optical unit and allows for easy conjugation of linkers that can include fluorescent organic dyes for an additional optical unit (F-SERS dots). In use, M-SERS dots allow for the separation of target cancer or cancer stem cells with an external magnetic field, while F-SERS dots can rapidly locate specific proteins within large areas of tissue and simultaneously analyze multiple targets based on their Raman signals. Moreover, NIR SERS dots can be detected with a high sensitivity within deep tissues, thus allowing them to be applied to in vivo multiplex detection. As none of these advanced functional SERS dots exhibit any sign of cytotoxicity for cell lines, they demonstrate a clear potential for more efficient, high-throughput screening of biological molecules using Raman technology.