Organic Rankine cycle (ORC) systems are a class of distributed power-generation systems that are suitable for the efficient conversion of low-to-medium temperature thermal energy to useful power. These versatile systems have significant potential to contribute in diverse ways to future clean and sustainable energy systems through, e.g., deployment for waste-heat recovery in industrial facilities, but also the utilisation of renewable-heat sources, thereby improving energy access and living standards, while reducing primary energy consumption and the associated emissions. The energetic and economic performance, but also environmental sustainability of ORC systems, all depend strongly on the working fluid employed, and therefore a significant effort has been made in recent years to select, but also to design novel working fluids for ORC systems. In this context, computer-aided molecular design (CAMD) techniques have emerged as highly promising approaches with which to explore the key role of working fluids, and present an opportunity, by focusing on the design of new eco-friendly fluids with low environmental footprints, to identify alternatives to traditional refrigerants with improved characteristics. In this review article, an overview of working-fluid and system optimisation methodologies that can be used for the design and operation of next-generation ORC systems is provided. With reference to wide-ranging applications from waste-heat recovery in industrial and automotive applications, to biomass, geothermal and solar-energy conversion and/or storage, this review represents a comprehensive, forward-looking exposition of the application of CAMD to the design of ORC technology.