Surface-enhanced Raman scattering (SERS) enhancement and the reproducibility of the SERS signal strongly reflect the quality and nature of the SERS substrates because of diverse localized surface plasmon resonance (LSPR) excitations excited at interstitials or sharp edges. LSPR excitations are the most important ingredients for achieving huge enhancements in the SERS process. In this report, we introduce several gold and silver nanoparticle-based SERS-active substrates developed solely by us and use these substrates to investigate the influence of LSPR excitations on SERS. SERS-active gold substrates were fabricated by immobilizing colloidal gold nanoparticles on glass slides without using any surfactants or electrolytes, whereas most of the SERS-active substrates that use colloidal gold/silver nanoparticles are not free of surfactant. Isolated aggregates, chain-like elongated aggregates and two-dimensional (2D) nanostructures were found to consist mostly of monolayers rather than agglomerations. With reference to correlated LSPR and SERS, combined experiments were carried out on a single platform at the same spatial position. The isolated aggregates mostly show a broadened and shifted SPR peak, whereas a weak blue-shifted peak is observed near 430 nm in addition to broadened peaks centered at 635 and 720 nm in the red spectral region in the chain-like elongated aggregates. In the case of 2D nanostructures, several SPR peaks are observed in diverse frequency regions. The characteristics of LSPR and SERS for the same gold nanoaggregates lead to a good correlation between SPR and SERS images. The elongated gold nanostructures show a higher enhancement of the Raman signal than the the isolated and 2D samples. In the case of SERS-active silver substrates for protein detection, a new approach has been adopted, in contrast to the conventional fabrication method. Colloidal silver nanoparticles are immobilized on the protein functionalized glass slides, and further SERS measurements are carried out based on LSPR excitations. A new strategy for the detection of biomolecules, particularly glutathione, under aqueous conditions is proposed. Finally, supramolecular J-aggregates of ionic dyes incorporated with silver colloidal aggregates are characterized by SERS measurements and correlated to finite-difference time-domain analysis with reference to LSPR excitations.