X-ray computed tomography (CT) is widely used in various fields, including medical, industrial, and fundamental scientific applications. Its quick ability to provide three-dimensional quantification of structures makes it a valuable tool. In addition to patient diagnostics, CT methods are employed for the investigation of varied samples. This includes in-depth analysis using high-resolution micro- and nano-CT imaging. However, X-ray CT techniques not only perform morphological characterization but also allow for the direct evaluation of the effective atomic number (Zeff) and mass density (rho) of the subject under investigation. These techniques collectively fall within the class of Spectral CT methods, encompassing single-energy, dual-energy, differential phase contrast, and photon counting detector CT. Spectral CT leverages data acquired from different radiation interaction phenomena to map Zeff and rho values. This paper presents a comprehensive overview of these methodologies, elucidating the underlying theory behind each. Furthermore, we review published studies centered on the development of theoretical formulations and diverse applications of the techniques. They cover formalism development, calibration methods, and reconstruction algorithms. Additionally, we introduce the commonly utilized equipment along with case studies in medical, mineralogical, and material fields, as well as biology and archaeology. These case studies will be thoroughly evaluated and discussed within the context of this paper.