The illumination of aggregated metal nanospecies can create strong local electric fields to brighten Raman scattering. This study describes a procedure to self-assemble gold nanorods (NRs) through the use of porphyrin and phthalocyanine agents to create reproducibly stable and robust NR aggregates in the form of end-to-end oligomers. Narrow inter-rod gaps result, creating electric field "hot spots" between the NRs. The organic linker molecules themselves are potential Raman-based optical labels, and the result is significant numbers of Raman-active species located in the hot spots. NR polymerization was quenched by phospholipid encapsulation, which allows for control of the polydispersity of the aggregate solution, to optimize the surface-enhanced Raman scattering (SERS) enhancement and permitted the aqueous solubility of the aggregates. The increased presence of Raman-active species in the hot spots and the optimizing of solution polydispersity resulted in the observation of scattering enhancements by encapsulated porphyrins/phthalocyanines of up to 3500-fold over molecular chromophores lacking the NR oligomer host.