The hypothesis of this paper is that in order to identify least cost solutions of the integration of fluctuating renewable energy sources into current or future 100% renewable energy supplies one has to take a Smart Energy Systems approach. This paper outline why and how to do so. Traditionally, significant focus is put on the electricity sector alone to solve the renewable energy integration puzzle. Smart grid research traditionally focuses on ICT, smart meters, electricity storage technologies, and local (electric) smart grids. In contrast, the Smart Energy System focuses on merging the electricity, heating and transport sectors, in combination with various intra-hour, hourly, daily, seasonal and biannual storage options, to create the flexibility necessary to integrate large penetrations of fluctuating renewable energy. However, in this paper we present the development and design of coherent Smart Energy Systems as an integrated part of achieving future 100% renewable energy and transport solutions. The transition from fossil fuels towards the integration of more and more renewable energy requires rethinking and redesigning the energy system both on the generation and consumption side. To enable this, the Smart Energy System must have a number of appropriate infrastructures for the different sectors of the energy system, which are smart electricity grids, smart thermal grids (district heating and cooling), smart gas grids and other fuel infrastructures. It enables fluctuating renewable energy (such as wind, solar, wave power and low value heat sources) to utilise new sources of flexibility such as solid, gaseous, and liquid fuel storage, thermal storage and heat pumps and battery electric vehicles. Smart Energy Systems also enable a more sustainable and feasible use of bioenergy than the current types allow. It can potentially pave the way to a bioenergy-free 100% renewable energy and transport system.