Through the years, stochastic physics has provided important insight into natural phenomena that possess an inherently random nature. From its foundations in the study of Brownian motion up through its myriad present applications, a stochastic description of nature has yielded an elegant theoretical understanding, as well as providing practical and efficient simulation techniques. One particularly important application is to the field of quantum optics, in which the interaction of light and matter is treated in a fundamentally quantum-mechanical manner. The work presented here utilizes the methods of stochastic physics to understand a variety of quantum-optical phenomena involving the dynamics of atoms interacting with photons. A solid theoretical understanding of such phenomena is often necessary to describe laser cooling of atoms, and many such applications are discussed here. A detailed model of atoms with complex internal structure interacting with three-dimensional laser fields is presented, as well as the rich dynamics of three-level atoms interacting with two lasers. Applications to cavity cooling of atoms and molecules are discussed, and a method for describing non-Markovian dynamics using relaxation techniques is presented. A novel cooling scheme utilizing Feshbach resonances in the scattering of two atoms is also treated.