The ability to control the organisation of, and interactions between, atoms, molecules and other nanoscale matter in functional, high-dimensional arrays has been identified as a crucial step towards the development of numerous future technologies and applications. Gold nanoparticles, due to their fascinating optical and catalytic properties, are therefore key candidates for the realisation of this goal. They can be used in isolation or in combination with other nanoscopic materials (single- and multi-walled carbon nanotubes and alternative metallic, semiconducting or insulating nanoparticles/rods) and have been shown to assemble into complex functional superstructures. Through synthesis, modification and characterisation (UV-vis, NMR and IR spectroscopies, transmission electron microscopy and dynamic light scattering) of novel functionalised nanostructures, we have been able to study their behaviour in solution and establish molar absorption coefficients for numerous species, allowing accurate determination of effective solution-phase concentration and nanoparticle size. This has allowed us to probe the specific nature and strength of the interactions (van der Waals, electrostatic, charge-transfer, covalent, osmotic, elastic) responsible for the complex binary architectures observed following self-assembly of gold nanoparticles and other nanoscale entities in solution, specifically those involved in the assembly of periodic superlattices of gold and silica nanoparticles and disordered arrays of gold nanoparticles and carbon nanotubes. We have shown that the type, stoichiometry and dimensionality of these nanoscale materials can be discretely tuned by appreciating and controlling the surface chemistry of the component parts. The figure shows schematic representations and related electron micrographs of the two systems under investigation.