The incorporation of silica nanoparticles (Si-NPs) into the polymer matrix is a growing area of interest research to produce high-performance polymer nanocomposites (NCs) across a wide range of nanotechnology applications. This improvement is due to the Si-NPs capability to self-assembly giving rise to specific well-organized structures with both short- and long-range order across a hierarchy of spatial scales, determined by both NP-NP and NP-matrix interactions, involving a careful balance among attractive driving forces, repulsive forces, and directional forces. Respect to this, the aim of the present paper is to systematically review the use of Si-NPs in polymer NCs and on the role of NPs self-assembly in determining the final material properties. Firstly, we explored the synthesis and modification of both isotropic and anisotropic Si-NPs in relation with use in NC materials, focusing on NPs dispersion and distribution, as well as on the functionalization strategies of Si-NPs. Besides Si-NPs functionalization with conventional small organic molecules, a large section is devoted to an emerging class of functionalized Si-NPs with macromolecules, namely silica hairy NPs (Si-HNPs), able to give rise a rich variety of complex assemblies and materials with new structures and functionalities. Successively, NCs materials containing Si-NPs and Si-HNPs have been explored in terms of synthetic preparation and properties. The self-organization of Si-NPs and Si-HNPs in polymer matrices has been reported and its effect on the functional materials properties have been evaluated with a critical point of view on the results, limits, and future perspectives. Our review can be considered a tutorial work, aiming at providing useful insights to researchers in the field of nanotechnology and nanoscience, taking into consideration the fundamental role of NPs self-assembly processes in determining the functional material properties.