Modern complex dynamical systems typically possess a multiechelon hierarchical hybrid structure characterized by continuous-time dynamics at the lower-level units and logical decision-making units at the higher-level of hierarchy. Hybrid dynamical systems involve an interacting countable collection of dynamical systems defined on subregions of the partitioned state space. Thus, in addition to traditional control systems, hybrid control systems involve supervising controllers which serve to coordinate the (sometimes competing) actions of the lower-level controllers. A subclass of hybrid dynamical systems are impulsive dynamical systems which consist of three elements, namely, a continuous-time differential equation, a difference equation, and a criterion for determining when the states of the system are to be reset. One of the main topics of this dissertation is the development of stability analysis and control design for impulsive dynamical systems. Specifically, we generalize Poincare's theorem to dynamical systems possessing left-continuous flows to address the stability of limit cycles and periodic orbits of left-continuous, hybrid, and impulsive dynamical systems. For nonlinear impulsive dynamical systems, we present partial stability results, that is, stability with respect to part of the system's state. Furthermore, we develop adaptive control framework for general class of impulsive systems as well as energy-based control framework for hybrid port-controlled Hamiltonian systems. Extensions of stability theory for impulsive dynamical systems with respect to the nonnegative orthant of the state space are also addressed in this dissertation. Furthermore, we design optimal output feedback controllers for set-point regulation of linear nonnegative dynamical systems. Another main topic that has been addressed in this research is the stability analysis of large-scale dynamical systems. Specifically, we extend the theory of vector Lyapunov functions by constructing a generalized comparison system whose vector field can be a function of the comparison system states as well as the nonlinear dynamical system states. Furthermore, we present a generalized convergence result which, in the case of a scalar comparison system, specializes to the classical Krasovskii-LaSalle invariant set theorem. Moreover, we develop vector dissipativity theory for large-scale dynamical systems based on vector storage functions and vector supply rates. Finally, using a large-scale dynamical systems perspective, we develop a system-theoretic foundation for thermodynamics. Specifically, using compartmental dynamical system energy flow models, we place the universal energy conservation, energy equipartition, temperature equipartition, and entropy nonconservation laws of thermodynamics on a system-theoretic basis.