Open-source APOST-3D software features a large number of wavefunction analysis tools developed over the past 20 years, aiming at connecting classical chemical concepts with the electronic structure of molecules. APOST-3D relies on the identification of the atom in the molecule (AIM), and several analysis tools are implemented in the most general way so that they can be used in combination with any chosen AIM. Several Hilbert-space and real-space (fuzzy atom) AIM definitions are implemented. In general, global quantities are decomposed into one- and two-center terms, which can also be further grouped into fragment contributions. Real-space AIM methods involve numerical integrations, which are particularly costly for energy decomposition schemes. The current version of APOST-3D features several strategies to minimize numerical error and improve task parallelization. In addition to conventional population analysis of the density and other scalar fields, APOST-3D implements different schemes for oxidation state assignment (effective oxidation state and oxidation states localized orbitals), molecular energy decomposition schemes, and local spin analysis. The APOST-3D platform offers a user-friendly interface and a comprehensive suite of state-of-the-art tools to bridge the gap between theory and experiment, representing a valuable resource for both seasoned computational chemists and researchers with a focus on experimental work. We provide an overview of the code structure and its capabilities, together with illustrative examples.