The Helmholtz-Hodge Decomposition (HHD) describes the decomposition of a flow field into its divergence-free and curl-free components. Many researchers in various communities like weather modeling, oceanology, geophysics, and computer graphics are interested in understanding the properties of flow representing physical phenomena such as incompressibility and vorticity. The HHD has proven to be an important tool in the analysis of fluids, making it one of the fundamental theorems in fluid dynamics. The recent advances in the area of flow analysis have led to the application of the HHD in a number of research communities such as flow visualization, topological analysis, imaging, and robotics. However, because the initial body of work, primarily in the physics communities, research on the topic has become fragmented with different communities working largely in isolation often repeating and sometimes contradicting each others results. Additionally, different nomenclature has evolved which further obscures the fundamental connections between fields making the transfer of knowledge difficult. This survey attempts to address these problems by collecting a comprehensive list of relevant references and examining them using a common terminology. A particular focus is the discussion of boundary conditions when computing the HHD. The goal is to promote further research in the field by creating a common repository of techniques to compute the HHD as well as a large collection of example applications in a broad range of areas.