Large-scale unsteady flow structures play an influential role in the dynamics of many practical flows, such as those found in gas turbine combustion chambers. This thesis is concerned primarily with large-scale unsteady structures that arise due to self-sustained hydrodynamic oscillations, also known as global hydrodynamic instability. Direct numerical simulation (DNS) of the Navier--Stokes equations in the low Mach number limit is used to obtain a steady base flow, and the most unstable direct and adjoint global modes. These are combined, using a structural sensitivity framework, to identify the region of the flow and the feedback mechanisms that are responsible for causing the global instability. Using a Lagrangian framework, the direct and adjoint global modes are also used to identify the regions of the flow where steady and unsteady control, such as a drag force or heat input, can suppress or promote the global instability. These tools are used to study a variety of reacting and non-reacting flows to build an understanding of the physical mechanisms that are responsible for global hydrodynamic instability in swirling diffusion flames. In a non-swirling lifted jet diffusion flame, two modes of global instability are found. The first mode is a high-frequency mode caused by the instability of the low-density jet shear layer in the premixing zone. The second mode is a low-frequency mode caused by an instability of the outer shear layer of the flame. Two types of swirling diffusion flames with vortex breakdown bubbles are considered. They show qualitatively similar behaviour to the lifted jet diffusion flames. The first type of flame is unstable to a low-frequency mode, with wavemaker located at the flame base. The second type of flame is unstable to a high-frequency mode, with wavemaker located at the upstream edge of the vortex breakdown bubble. Feedback from density perturbations is found to have a strong influence on the unstable modes in the reacting flows. The wavemaker of the high-frequency mode in the reacting flows is very similar to its non-reacting counterpart. The low-frequency mode, however, is only observed in the reacting flows. The presence of reaction increases the influence of changes in the base flow mixture fraction profiles on the eigenmode. This increased influence acts through the heat release term. These results emphasize the possibility that non-reacting simulations and experiments may not always capture the important instability mechanisms of reacting flows, and highlight the importance of including heat release terms in stability analyses of reacting flows.