Encapsulation of different guest-species such as molecules and ions inside carbon nanotubes (CNTs) has been reported in the literatures during the last 15 years and represents an exciting development of nanoengineering of novel materials and composites. The reported nanocomposite materials show the semi-conducting properties with potential applications in nanosensors, nanounits and nanocircuits as well as advanced energy transfer and storage properties, and encompass manufacturing for novel nanowires, nanoelectronic devices with properties designed with optoelectronic, spintronic and nanomagnetic qualities. This review reports on a wide range of encapsulation references with particular focus on single molecules, atomic chains, metal halides and polymers encapsulated inside CNTs. The encapsulation methods and the chemical and physical qualities of these novel materials are crucial for the future manufacturing of novel innovations in nanotechnology, and represent therefore the current state-ofthe-art of encapsulation methods in advanced manufacturing.