Small clusters of nanoparticles are ideal substrates for SERS measurements, but the SERS signal enhancement by a particular cluster is strongly dependent on its structural characteristics and the measurement conditions. Two methods for high-throughput assembly of silver nanocubes into small clusters at predetermined locations on a substrate are presented. These fabrication techniques make it possible to study both the structure and the plasmonic properties of hundreds of nanoparticle clusters. The variations in SERS enhancement factors from cluster to cluster were analyzed and correlated with cluster size and configuration, and laser frequency and polarization. Using Raman instruments with 633 nm and 785 nm lasers and linear clusters of nanocubes, an increase in the reproducibility of the enhancement and an increase in the average enhancement values were achieved by increasing the number of nanocubes in the cluster, up to 4 nanocubes per cluster. By examining the effect of cluster configuration, it is shown that linear clusters with nanocubes attached in a face-to-face configuration are not as effective SERS substrates as linear clusters in which nanocubes are attached along an edge.