Photoactive pi-conjugated molecules (quaterthiophene and phthalocyanine) are either encapsulated into the hollow core of single-walled carbon nanotubes or noncovalently stacked at their outer surface in order to elaborate hybrid nanosystems with new physical properties, providing practical routes to fit different requirements for potential applications. We are interested in the relationship between the structure and the optoelectronic properties. The structural properties are investigated mainly by x-ray diffraction and/or transmission electron microscopy and Raman spectroscopy. We show that the supramolecular organizations of confined quaterthiophenes depend on the nanocontainer size, whereas phthalocyanine encapsulation leads to the formation of a one-dimensional phase for which the angle between the molecule ring and the nanotube axis is close to 32 deg. Confined phthalocyanine molecules display Raman spectra hardly altered with respect to the bulk phase, suggesting a rather weak interaction with the tubes. In contrast, the vibrational properties of the molecules stacked at the outer surface of tubes display important modifications. We assume a significant curvature of the phthalocyanine induced by the interaction with the tube walls and a change of the central atom position within the molecular ring, in good agreement with our density functional theory calculations.