A gap mode in surface enhanced Raman scattering (SERS) can provide single molecule sensitivity and spatial resolution of a few nanometers. To establish a gap mode Raman spectroscopy, we investigated three distinct geometries of a flocculate of silver nanoparticles (AgNP), a gap mode with a metal substrate/molecule/metal nanoparticle sample under an external, and attenuated total reflection (ATR) geometry. We succeeded to elucidate adsorbed state of different thiol molecules in flocculates of AgNPs as well as counter ions in solutions. A large number of AgNPs were immobilized on Ag films via various thiol molecules using van der Waals and electrostatic interaction, which provided enormous SERS enhancement of 10⁸-10⁹ at a nanogap. A propagating surface plasmon (PSP) combined with a gap mode under ATR geometry yielded significantly larger SERS enhancement than that under an external geometry.