This review presents the state of the art of molecular simulation and theory of adsorption, intrusion and freezing in porous silica. Both silica pores of a simple geometry and disordered porous silicas which exhibit morphological and topological disorders are considered. We provide a brief description of the numerical models of porous silicas available in the literature and present the most common molecular simulation and theoretical methods. Adsorption in regular and irregular pores is discussed in the light of classical theories of adsorption and capillary condensation in pores. We also present the different evaporation mechanisms for disordered systems: pore blocking and cavitation. The criticality of fluids confined in pores, which is still the matter of debate, is then discussed. We review theoretical results for intrusion/extrusion and freezing in silica pores and discuss the validity of classical approaches such as the Washburn-Laplace equation and Gibbs-Thomson equation to describe the thermodynamics of intrusion and in-pore freezing. The validity of the most widely used characterization techniques is then discussed. We report some concluding remarks and suggest directions for future work.