Microalgae are a diverse group of single-cell photosynthetic organisms, both prokaryotes and eukaryotes, which can rapidly grow in a wide range of habitats under photoautotrophic conditions. Recently, microalgae have been the object of increasing interest due to the attractive potential they offer in the current scenario of dwindling energy and food resources. Microalgae are flexible systems with the potential for production of feedstock biomass and high valuable natural products. Their productivities may be further improved with strain selection, genetic amelioration, and process engineering. However, though microalgae are considered the best alternative feedstock for the production of 3rd generation biofuel, the high cost of biomass production and biorefinery currently makes them uncompetitive with the cost of fossil fuels and traditional renewable energy resources. The development of microalgae culture technologies at commercial scale is, therefore, limited to a few profitable facilities around the world, producing very high value products (e.g., carotenoids, poly unsaturated fatty acids, immune-stimulants polysaccharides, etc.), whose high selling price can guarantee the return on investment. Our review deals with currently known natural high value products from microalgae, divided according to their potential use (i.e., energy- and non-energy based), their target market, and their cost-benefit balance beyond the biomass production. We analyze the economics of algal feedstock production and biorefinery, together with an overall energetic effectiveness of the cultivation process.