Surface-enhanced Raman scattering (SERS) techniques offer a number of advantages in molecular detection and analysis, particularly in terms of the multiplex detection of biomolecules. So far, many new SERS-based substrates and analytical techniques have been reported. For easy understanding, various SERS techniques are classified into the following four categories: adsorption-mediated direct detection; antibody- or ligand-mediated direct detection; binding catalyzed indirect detection; and tag-based indirect detection. Among these, recent successes of SERS tagging/encoding (nano/micro) materials and detection methods are highlighted, including our recent works. Some novel SERS-based strategies for the detection of several biological molecules are also introduced.