The Estrada index of a graph/network is defined as the trace of the adjacency matrix exponential. It has been extended to other graph-theoretic matrices, such as the Laplacian, distance, Seidel adjacency, Harary, etc. Here, we describe many of these extensions, including new ones, such as Gaussian and Mittag-Leffler ones. More importantly, we contextualize all of these indices in physico-mathematical frameworks which allow their interpretations and facilitate their extensions and further studies. We also describe several of the bounds and estimations of these indices reported in the literature and analyze many of them computationally for small graphs as well as large complex networks. This review article is intended to formalize many of the Estrada indices proposed and studied in the mathematical literature serving as a guide for their further studies.