The aim of this research was to achieve the post-synthetic modification of peripherally functionalised organic cages to access novel cage architectures, including cage rotaxane systems, using the copper(I)-catalysed azide-alkyne cycloaddition (CuAAC) reaction, and to investigate their properties and potential applications. In this work, a family of novel, amine-based, alkyne-functionalised organic cages were successfully synthesised. This enabled a comprehensive study of their thermal, sorption, optical, and structural properties using various analytical techniques. The presence of alkyne groups on the periphery of the cage structures facilitated their post-synthetic modification via the CuAAC reaction. This peripheral modification was exploited in two main directions: (1) to introduce a range of functional groups onto the exterior of the cage structure, and (2) to synthesise organic cage[n]rotaxane systems, in which the internal cavity remained unoccupied. The functionalised cages were analysed for their thermal, sorption, and structural properties, and selected examples were further investigated for specific applications, including photoswitching, hydrogen-bonded organic framework assembly, host–guest binding, and transition metal complex formation. The organic cage[n]rotaxane systems were similarly characterised and compared to their non-interlocked congeners in terms of thermal stability, sorption behaviour, structural features, and solubility. Finally, the rotaxanation methodology was extended to a more complex rotaxane system comprising two cages.