Topological data analysis (TDA) is a rapidly evolving field in applied mathematics and data science that leverages tools from topology to uncover robust, shape-driven, and explainable insights in complex datasets. The main workhorse is persistent homology, a technique rooted in algebraic topology. Paired with topological deep learning (TDL) or topological machine learning, persistent homology has achieved tremendous success in a wide variety of applications in science, engineering, medicine, and industry. However, persistent homology has many limitations due to its high-level abstraction, insensitivity to non-topological changes, and restriction to point cloud data. This paper presents a comprehensive review of TDA and TDL beyond persistent homology. It analyzes how persistent topological Laplacians and Dirac operators provide spectral representations to capture both topological invariants and homotopic evolution. Other formulations are presented in terms of sheaf theory, Mayer topology, and interaction topology. For data on differentiable manifolds, techniques rooted in differential topology, such as persistent de Rham cohomology, persistent Hodge Laplacian, and Hodge decomposition, are reviewed. For one-dimensional (1D) curves embedded in 3-space, approaches from geometric topology are discussed, including multiscale Gauss-link integrals, persistent Jones polynomials, and persistent Khovanov homology. This paper further discusses the appropriate selection of topological tools for different input data, such as point clouds, sequential data, data on manifolds, curves embedded in 3-space, and data with additional non-geometric information. A review is also given of various topological representations, software packages, and machine learning vectorizations. Finally, this review ends with concluding remarks.