The novel concept of Smart Energy Systems has emerged over the last decade within the context of the energy transition toward a carbon-free sustainable future. For an energy system to be "smart", several factors have to converge: (i) a high integration of renewable energy sources, (ii) the flexibility required to deal with their fluctuating nature, (iii) the exploitation of digital technologies and (iv) the cross-sectoral approach that uses synergies between various energy domains (sector coupling). Indeed, the traditional domain-specific energy flows from production to usage are overcome in favor of an integrated approach, in which energy is converted or stored into the most convenient vector. Coupling energy sectors, however, requires smart management and control strategies that are able to drive a system toward minimal energy use (or minimal cost), despite its increased complexity. Furthermore, the advanced management strategy of a smart energy system may vary significantly depending on its spatial dimensions, from the national/regional level to small-scale energy communities or islands. Hence, pointing out the latest progress on smart management is paramount for orienting future research and practice, and fostering the energy transition. This work reviews the available methods and tools for enabling the optimal operation of smart energy systems at different spatial and temporal scales. They are categorized according to relevant features such as the energy vectors and infrastructures involved, the presence of short-term or seasonal storage, the time horizon and specific application. The paper also summarizes research guidelines and drivers for the continuous development and expansion of smart energy systems at all levels. It was found particularly relevant to investigate optimal management at multiple time and space scales at the same time, for exploiting not only synergies between sectors, but also between neighboring communities. The tools should also have the possibility to include additional energy vectors (e.g. different types of chemicals) and their verification in demonstration cases should be promoted.