Conjugated polymers (CPs) are widely used for a variety of applications as a result of their high quantum yields, strong extinction coefficients, and good stability to a variety of experimental conditions. In many cases, the use of conjugated polymer nanoparticles (CPNs) provides additional practical advantages. The ability to understand how the structure of the CP affects its photophysical properties has the potential to significantly accelerate research in this area. In this work we examine 3 CPs, including two novel polymer architectures, and evaluate how the structures of the conjugated side chains affect the photophysical properties of the free polymer chains as well as the properties of aggregated CPNs. Both the linker identity and the terminal aromatic rings of the side chains were found to affect the photophysical properties of the CPs, with the terminal groups leading to the most substantial changes in photophysical properties in all of the polymeric forms (well-solubilized in organic solvent and aggregated in nanoparticles).