Encapsulation systems are urgently needed both as micrometer and sub-micrometer capsules for active chemicals' delivery, to encapsulate biological objects and capsules immobilized on surfaces for a wide variety of advanced applications. Methods for encapsulation, prolonged storage and controllable release are discussed in this review. Formation of stimuli responsive systems via layer-by-layer (LbL) assembly, as well as via mobile chemical bonding (hydrogen bonds, chemisorptions) and formation of special dynamic stoppers are presented. The most essential advances of the systems presented are multifunctionality and responsiveness to a multitude of stimuli – the possibility of formation of multi-modal systems. Specific examples of advanced applications – drug delivery, diagnostics, tissue engineering, lab-on-chip and organ-on-chip, bio-sensors, membranes, templates for synthesis, optical systems, and antifouling, self-healing materials and coatings – are provided. Finally, we try to outline emerging developments.