Functionalized aligned and non-aligned carbon nanotubes (CNTs) have demonstrated outstanding physicochemical properties for a wide range of potential applications in energy conversion and storage, environmental remediation, and health care. In this review, we systematically summarize numerous innovative strategies developed for both covalent and non-covalent, functionalization of aligned and non-aligned CNTs with various heteroatom dopants, functional groups, small molecules, and/or macromolecules. Different unique chemical functionalization approaches reported for aligned CNTs include asymmetric and tube length-specific functionalization, multicomponent micropatterning, and end-opening for encapsulation/inner-wall modification. With a broader scope, we cover current challenges and future perspectives of CNTs in exciting new emerging fields, ranging from electrochemical catalysis for energy conversion/storage and environment protection, through sensing, to biomedical technologies.