For efficient utilization of surface plasmons in surface enhanced Raman scattering (SERS), we investigated the gap modes in flocculates of metal nanoparticles (MNPs), and between MNPs and metal substrates under an external and an attenuated total reflection (ATR) geometry. First, the adsorbed state of thiol molecules and counter ions trapped in solutions were elucidated using flocculation-SERS, in which closely adjacent nanoparticles are formed by using interactions between MNPs and target species. Second, we obtained a pronounced enhancement of 10⁵–10⁸ at a nanogap between gold nanoparticles (AuNPs) and various metal substrates even with a large damping under an external geometry. Markedly larger enhancement was obtained for larger AuNPs, by a factor of 10³ for particles with a radius (r) of 50 nm compared with those of r = 15 nm in this geometry. Finally, we attained an additional enhancement factor under an ATR geometry by a coupling of propagating surface plasmons with gap modes.