After over 30 years of development, surface-enhanced Raman spectroscopy (SERS) is now facing a very important stage in its history. The explosive development of nanoscience and nanotechnology has assisted the rapid development of SERS, especially during the last 5 years. Further development of surface-enhanced Raman spectroscopy is mainly limited by the reproducible preparation of clean and highly surface enhanced Raman scattering (SERS) active substrates. This review deals with some substrate-related issues. Various methods will be introduced for preparing SERS substrates of Ag and Au for analytical purposes, from SERS substrates prepared by electrochemical or vacuum methods, to well-dispersed Au or Ag nanoparticle sols, to nanoparticle thin film substrates, and finally to ordered nanostructured substrates. Emphasis is placed on the analysis of the advantages and weaknesses of different methods in preparing SERS substrates. Closely related to the application of SERS in the analysis of trace sample and unknown systems, the existing cleaning methods for SERS substrates are analyzed and a combined chemical adsorption and electrochemical oxidation method is proposed to eliminate the interference of contaminants. A defocusing method is proposed to deal with the laser-induced sample decomposition problem frequently met in SERS measurement to obtain strong signals. The existing methods to estimate the surface enhancement factor, a criterion to characterize the SERS activity of a substrate, are analyzed and some guidelines are proposed to obtain the correct enhancement factor.