After the continuous development of CMOS technology driven by transistor miniaturization and Moore’s law, the scientific community is witnessing the exploration of emerging paradigms to find new ways to develop computational systems. This paper presents critical concepts for understanding some of these new nanocomputing technologies, specifically field-coupled, quantum-dot cellular automata, nanomagnetic logic, silicon dangling bounds, photonic crystal logic, and DNA computing. Next, it shows emerging design automation tools for each of these areas and how they can be applied to support the development of new computing systems. The level of maturity and production speed of solutions achieved by conventional silicon technology thanks to very efficient electronic design automation (EDA) is remarkable. However, here we are dealing with technologies still in their infancy. Therefore, improvements in design automation tools are undoubtedly a way to accelerate the growth of new substrate alternatives and modern applications.