As the underlying causes of several neuronal disorders and neurodegenerative diseases still remain, to some extent, unknown and no accurate diagnostic tests are available, the identification of prognostic and predictive neurophysiological biomarkers has attracted tremendous interest. The continuous advancement of neuroscience methods applied in EEG and magnetoencephalography has been successful in capturing brain processes and identifying persistent cognitive deficits. In this article, the most promising approaches of this rapidly evolving field, along with some indicative clinical applications in major neuropathophysiological disorders, are reviewed. Such strategies for biomarker identification will lead the way to future clinical applications even if, currently, EEG biomarkers are in a premature state.