Recent developments in the fabrication of core-shell polymer nanocapsules, as well as their current and future applications, are reported here. Special attention is paid to the newly introduced surfactant-free fabrication method of aqueous dispersions of nanocapsules with hydrophobic liquid cores stabilized by amphiphilic copolymers. Various approaches to the efficient stabilization of such vehicles, tailoring their cores and shells for the fabrication of multifunctional, navigable nanocarriers and/or nanoreactors useful in various fields, are discussed. The emphasis is placed on biomedical applications of polymer nanocapsules, including the delivery of poorly soluble active compounds and contrast agents, as well as their use as theranostic platforms. Other methods of fabrication of polymer-based nanocapsules are briefly presented and compared in the context of their biomedical applications.